Post medconfig report, maybe there's something that's causing the issue.
Only games that work are silkworm and SWIV

It's not a hardware issue, something software is causing the problem.
I've just reloaded from scratch Picasso96 2.1b and the Mediator.
Anyway report below :
*** Envarc: variable settings: ***
MMU = Yes, previous setting: Yes
NoCache = Not Set, previous setting: Not Set
Emulation = Not Set, previous setting: Not Set
Buster = Not Set, previous setting: Not Set
RadeonMem = 32, previous setting: 32
VoodooMem = 12, previous setting: 12
VoodooInt = Yes, previous setting: Yes
VirgeMem = Not Set, previous setting: Not Set
VirgeInt = Not Set, previous setting: Not Set
Warp3D = Yes, previous setting: Yes
Gfxaddr = Not Set, previous setting: Not Set
Force = Not Set, previous setting: Not Set
Terminator = Not Set, previous setting: Not Set
Memsize = Not Set, previous setting: Not Set
FastEthernet = 0, previous setting: 0
tv.prefs file name = Not Set, previous setting: Not Set
Tuner = Not Set, previous setting: Not Set
Background = Not Set, previous setting: Not Set
*** Mediator System Files versions: ***
pci.library - ver.9.7 (11632 bytes)
MediatorNET.device - ver.2.10 (6176 bytes)
Radeon.card - ver.2.12 (15936 bytes)
Voodoo.card - ver.4.30 (14768 bytes)
Virge.card - ver.1.13 (12064 bytes)
Vendors.txt - ver. info N/A (219437 bytes)
MedConfig - ver.1.9 (119295 bytes)
*** Mediator Multimedia CD Files versions: ***
FastEthernet.device - ver.1.21 (7024 bytes)
mixer.library - ver.1.11 (4016 bytes)
fm801.audio - ver.4.14 (4156 bytes)
FM801 - ver. info N/A (1180 bytes)
sb128.audio - ver.4.20 (6336 bytes)
SB128 - ver. info N/A (2032 bytes)
SBMixer - ver.1.4 (2004 bytes)
tv.library - ver.4.13 (10304 bytes)
TV - ver.1.4 (1956 bytes)
tv.vhi - file N/A
*** Spider Files versions: ***
poseidon.library - ver.4.4 (116112 bytes)
spider.device - ver.3.20 (18560 bytes)
DriveSpeed - ver.1.2 (1960 bytes)
*** Warp 3D files versions: ***
Warp3D.library - ver.4.2 (215888 bytes)
Warp3DPPC.library - file N/A
*** Warp 3D for A3/4000 files versions: ***
W3D_Picasso96.library - ver.4.2 (39216 bytes)
W3D_Picasso96_PPC.library - file N/A
W3D_AvengerBE.library - ver.4.2 (295716 bytes)
W3D_AvengerBE_PPC.library - file N/A
W3D_AvengerLE.library - ver.4.2 (282312 bytes)
W3D_AvengerLE_PPC.library - file N/A
*** MMU Warp 3D for A1200 files versions: ***
W3D_Picasso96MU.library - ver.4.2 (7936 bytes)
W3D_AvengerBEMU.library - ver.4.2 (279268 bytes)
W3D_AvengerLEMU.library - ver.4.2 (279296 bytes)
*** NO_MMU Warp 3D for A1200 files versions: ***
W3D_Picasso96M.library - ver.4.2 (12780 bytes)
W3D_Picasso96M_PPC.library - file N/A
W3D_AvengerBEM.library - ver.4.2 (535304 bytes)
W3D_AvengerBEM_PPC.library - file N/A
W3D_AvengerLEM.library - ver.4.2 (535388 bytes)
W3D_AvengerLEM_PPC.library - file N/A
*** Other files versions: ***
AmigaOS ROM Update - file N/A
rtg.library - ver.40.3992 (217988 bytes)
emulation.library - ver.40.389 (39652 bytes)
Picasso96API.library - ver.2.300 (24520 bytes)
ahi.device - ver.6.6 (83908 bytes)
68040.library - ver.60.1 (392 bytes)
68060.library - ver.43.1 (64820 bytes)
warp.library - file N/A
ppc.library - file N/A
*** Other files versions: ***
scsi.device - ver.50.0 (-1 bytes)
FastATA.driver - file N/A
ATA3.driver - ver.7.1 (18960 bytes)
4xEIDE.driver - file N/A
model - , gfx - , zorro - , pcmcia - ,
serial - , ppc - , mmu030 - , mmulib - ,
nocache - , emulation - , warp3d - , pci - .
startup-sequence:
; $VER: Startup-Sequence_AmiKit OS3.9 BB2
; Startup-Sequence for AmigaOS 3.9 + AmiKit (by Jan Zahurancik ©2005-2008)
; Modified to work with real Amiga by Retrofan
C:ATA3.driver RESIDENT QUIET
C:stack 8192
Run >NIL: C

RAP
if WARN
Run >NIL: C:RemAPollo QUIET
EndIf
C:Safe RENRAM OWNOUT MOUNTSIZE=6684 ;Checks for viruses
C:morelibspace
SetPatch SKIPROMUPDATES "scsi.device" QUIET
C:mcpramlibpatch
Run >NIL: C:wbm
Assign >NIL: Amikit: System:
;BootScreen by Joseph Luk
;BootScreen
;run >NIL: C

lay16 Priority 1 ;SYS

refs/Presets/Sounds/Opening_Theme_A.aiff
;C:Wait 5
;C:CyReq
C:BlazeWCP
C:StackAttack 32768 ;adds stack size to selected value
C

atchControl ;part of MCP
C:TagLiFE ;patches the utility.lirary
C:Version >NIL:
C:AddBuffers >NIL: DF0: 15
FailAt 21
C:MakeDir RAM:T RAM:Clipboards RAM:ENV RAM:ENV/Sys RAM:T/VC_TEMP
C:Copy >NIL: ENVARC: RAM:ENV ALL NOREQ
Resident >NIL: C:Assign PURE
Resident >NIL: C:Execute PURE
Assign >NIL: ENV: RAM:ENV
Assign >NIL: T: RAM:T
Assign >NIL: CLIPS: RAM:Clipboards
Assign >NIL: REXX: S:
Assign >NIL: PRINTERS: DEVS

rinters
Assign >NIL: KEYMAPS: DEVS:Keymaps
Assign >NIL: LOCALE: SYS:Locale
Assign >NIL: LIBS: SYS:Classes ADD
Assign >NIL: HELP: LOCALE:Help DEFER
Assign >NIL: L: SYS:Utilities/Expansion/SmartFileSystem/L ADD
Assign >NIL: A-Programs: SYS

rograms
Assign >NIL: A-Temp: SYS:Temp
C:FBlit
C:FText
IF $bbfix EQ "0" ;adjusts AmiKit if both BoingBags for OS3.9 were installed
version >NIL: Shell VERSION 45
IF NOT WARN
IF EXISTS SYS:WBStartup/AmiDock
IF EXISTS SYS:WBStartup/Disabled/AmiDock
Delete >NIL: SYS:WBStartup/Disabled/AmiDock FORCE QUIET
ENDIF
Rename >NIL: SYS:WBStartup/AmiDock TO SYS:WBStartup/Disabled/AmiDock QUIET
ENDIF
IF EXISTS SYS:WBStartup/ASyncWB
IF EXISTS SYS:WBStartup/Disabled/ASyncWB
Delete >NIL: SYS:WBStartup/Disabled/ASyncWB FORCE QUIET
ENDIF
Rename >NIL: SYS:WBStartup/ASyncWB TO SYS:WBStartup/Disabled/ASyncWB QUIET
Delete >NIL: SYS:WBStartup/ASyncWB.info
ENDIF
IF EXISTS SYS:WBStartup/BenchTrash
IF EXISTS SYS:WBStartup/Disabled/BenchTrash
Delete >NIL: SYS:WBStartup/Disabled/BenchTrash FORCE QUIET
ENDIF
Rename >NIL: SYS:WBStartup/BenchTrash TO SYS:WBStartup/Disabled/BenchTrash QUIET
ENDIF
IF EXISTS SYS:WBStartup/DefIcons
IF EXISTS SYS:WBStartup/Disabled/DefIcons
Delete >NIL: SYS:WBStartup/Disabled/DefIcons FORCE QUIET
ENDIF
Rename >NIL: SYS:WBStartup/DefIcons TO SYS:WBStartup/Disabled/DefIcons QUIET
ENDIF
Delete >NIL: SYS:Utilities/Amplifier#? FORCE ALL QUIET
Copy >NIL: SYS

refs/Presets/AmiKit/Install/System TO SYS: CLONE ALL QUIET
SetENV bbfix 1
Copy >NIL: ENV:bbfix TO ENVARC: CLONE QUIET
EndIF
EndIF
C:Version >NIL: SYS:Libs/xadmaster.library 12 1 FILE ;installs latest XAD if BoingBag1 for OS3.9 was installed only
IF WARN
Copy >NIL: SYS

refs/Presets/AmiKit/Install/System TO SYS: CLONE ALL QUIET
EndIF
C:Version >NIL: SYS:Classes/DataTypes/ilbm.datatype 44 26 FILE ;adjusts AmiKit if BoingBag35-2 was installed
IF WARN
Copy >NIL: SYS

refs/Presets/AmiKit/Install/System/Classes/DataTypes/ilbm.datatype TO SYS:Classes/Datatypes/ CLONE QUIET
EndIF
C:CPU60 B >NIL:
Run >NIL: CopyMem060
IF NOT EXISTS SYS:Fonts
Assign FONTS:
EndIF
BindDrivers ;useless on UAE
C:Mount >NIL: DEVS

OSDrivers/~(#?.info)
;C:LoadMonDrvs
;IF EXISTS DEVS:Monitors
; IF EXISTS DEVS:Monitors/VGAOnly
; DEVS:Monitors/VGAOnly
; EndIF
C:List >NIL: DEVS:Monitors/~(#?.info|VGAOnly) TO T:M LFORMAT "DEVS:Monitors/%s"
Execute T:M
C

elete >NIL: T:M
EndIF
;C

96-EmulationUpdate ;fakes the version info of emulated CGX libraries under Picasso96
;C

96Refresh >NIL: 100 ;set this value (100 by default) according to your monitor refresh rate and WinUAE display settings
;C

96Refresh
;SYS:Utilities/Expansion/ShowAmiga96/Bin/ShowAmiga96_Rev239C18 ;shows the picture during startup
SetEnv Language "english"
SetEnv Workbench $Workbench
SetEnv Kickstart $Kickstart
UnSet Workbench
UnSet Kickstart
C:AddDataTypes REFRESH QUIET
;Following two lines provide TrueType support. IMPORTANT: if you disable them you must enable C:WAIT line in front of C:IPREFS to avoid startup crashes!!!
;Assign >NIL: AfA_OS_Libs: SYS:Utilities/EXPANSION/AfA_OS/AfA_OS_Libs
;C:AfA_OS_Loader
;IF NOT EXISTS ENV:afa/replacevisualprefs ;enables the following lines only if similar featrues are disabled in AfA_OS
Run >NIL: SYS:Utilities/Expansion/TitleShadow/TitleShadow ;enables effects for window titlebar texts
Run >NIL: SYS:Utilities/Expansion/VisualPrefs/VisualPrefs ;enables the customization of Amiga GUI
Run >NIL: SYS:Utilities/Expansion/VisualPrefs/TRAP ALL ;enables the customization of Amiga ReAction GUI
;ENDIF
;C:Wait 3 ;prevents IPrefs from crashes. Increase the value if IPrefs still crashes.
C:IPrefs
;SYS:Utilities/Expansion/ShowAmiga96/Bin/ShowAmiga96_Login >NIL:
SYS:Utilities/Expansion/FullPalette/FPPrefs ;applies FullPalette settings
C:ConClip
;IF EXISTS C:CyberBugFix
; C:CyberBugFix
;EndIF
Path >NIL: RAM: C: SYS:Utilities SYS:Rexxc SYS:System S: SYS

refs SYS:WBStartup SYS:Tools SYS:Tools/Commodities SYS:Utilities/PicShow SYS:Utilities/EvenMore SYS:Utilities/MysticView SYS:Utilities/SimpleFind3 SYS:Utilities/Expansion/SmartFileSystem
IF NOT EXISTS ENV:afa/replacebirdie ;enables gfx patterns for windows borders (only if similar feature is disabled in AfA_OS)
C:Wait 3 ;prevents Birdie from not loading the background picture.
Run >NIL: SYS:Utilities/Expansion/Birdie/Birdie ? <Env:Birdie.prefs
ENDIF
SYS:System/REXXMast >NIL:
IF EXISTS S:User-Startup
Execute S:User-Startup
EndIF
IF EXISTS S:AmiKit-Startup
Execute S:AmiKit-Startup
EndIF
;following lines enable enchanced CLI/Shell functionality
IF EXISTS DEVS:KingCON-mountlist
Assign CON: DISMOUNT
Assign RAW: DISMOUNT
Mount CON: from DEVS:KingCON-mountlist
Mount RAW: from DEVS:KingCON-mountlist
ENDIF
Resident Execute REMOVE
Resident Assign REMOVE
C:Version >NIL: C:MakeLink 37 4 FILE
IF NOT WARN
C:Copy >NIL: ENVARC:SYS/def_RAM.info RAM

isk.info CLONE QUIET
ELSE
C:MakeLink >NIL: RAM

isk.info ENVARC:SYS/def_RAM.info SOFT
ENDIF
;Run >NIL: SYS:Utilities/Expansion/PowerIcons/PowerIcons >NIL: ;enables PNG icon support (Don't use it if AfA_OS_Loader is enabled!)
C:WBCtrl IMT=FAST MNL=100 ;tweaks Workbench
;Run >NIL: C:CPointer ;centers the mouse pointer on the screen (regardless of the screenmode used). Disable this entry if some of the other CPointer line is enabled.
;Run >NIL: C:CPointer XPOS=400 YPOS=368 MCLICK=50 ;for 800x600 screens, automatically clicks the Dopus "RUN" button
Run >NIL: C:CPointer XPOS=510 YPOS=455 MCLICK=50 ;for 1024x768 screens, automatically clicks the Dopus "RUN" button
;Run >NIL: C:CPointer XPOS=576 YPOS=500 MCLICK=50 ;for 1152x864 screens, automatically clicks the Dopus "RUN" button
;Run >NIL: C:CPointer XPOS=641 YPOS=579 MCLICK=50 ;for 1280x1024 screens, automatically clicks the Dopus "RUN" button
;Run >NIL: C:CPointer XPOS=797 YPOS=674 MCLICK=50 ;for 1600x1200 screens, automatically clicks the Dopus "RUN" button
;Run >NIL: C

atchAsl ;enables MUI file requesters
;C:ChangeExp ;prevents from identifying your system as UAE
IF EXISTS S:AmiKit-StartOS ;starts Magellan II, Scalos or Workbench - depends on your MorpheuZ settings.
Execute S:AmiKit-StartOS
ELSE
C:LoadDB SIMPLEGELS
EndIF
C:MemTrailer SIZE=96 ;provides partial memory protection
EndCLI >NIL:
PciInfo report:
Pci Device 1:
VendorID: $121a
VendorName: 3dfx Interactive Inc
DeviceID: $5
DeviceName: Voodoo3 All Voodoo3 chips, 3000
ClassCode: $30000
RevisionID: $1
InterruptPin: 2
SubsystemVendorID: $121a
SubsystemID: $57
MemSpace0: $80000000 - $81ffffff
MemSpace1: $82000000 - $83ffffff
IOSpace2: $ed6000 - $ed60ff
RomSpace: $84000000 - $8400ffff
Pci Device 2:
VendorID: $1274
VendorName: Ensoniq
DeviceID: $5000
DeviceName: ES1373 AudioPCI
ClassCode: $40100
RevisionID: $1
InterruptPin: 3
SubsystemVendorID: $4942
SubsystemID: $4c4c
IOSpace0: $ed6400 - $ed643f
Pci Device 3:
VendorID: $10ec
VendorName: Realtek Semiconductor
DeviceID: $8139
DeviceName: RTL-8139/8139C/8139C+ 10/100 Mbps Fast Ethernet NIC
ClassCode: $20000
RevisionID: $10
InterruptPin: 1
SubsystemVendorID: $149c
SubsystemID: $139a
IOSpace0: $ed6800 - $ed68ff
MemSpace1: $84010000 - $840100ff
RomSpace: $84020000 - $8402ffff
Pci Device 4:
VendorID: $1002
VendorName: ATI
DeviceID: $5960
DeviceName: RV280 Radeon 9200 Pro
ClassCode: $30000
RevisionID: $1
InterruptPin: 2
SubsystemVendorID: $18bc
SubsystemID: $891
MemSpace0: $90000000 - $9fffffff
IOSpace1: $ed6c00 - $ed6cff
MemSpace2: $84030000 - $8403ffff
RomSpace: $84040000 - $8405ffff
ShowConfig report:
PROCESSOR: CPU 68060/68060fpu/68060mmu
CUSTOM CHIPS: AA PAL Alice (id=$0023), AA Lisa (id=$00F8)
VERS: Kickstart version 40.68, Exec version 40.10, Disk version 45.5
RAM: Node type $A, Attributes $5 (FAST), at $1000000-$4FFFFFF (64.0 meg)
Node type $A, Attributes $2005 (FAST), at $92000000-$9FEFFFFF (223.0 meg)
Node type $A, Attributes $2005 (FAST), at $82C02C00-$82FFFFFF (~4.0 meg)
Node type $A, Attributes $703 (CHIP), at $1000-$1FFFFF (~2.0 meg)
BOARDS:
Board + ROM (HD?) (unidentified): Prod=8738/35($2222/$23) (@$EA0000 128K)
Board (Index Information Ltd): Prod=2206/60($89E/$3C) (@$EC0000 128K)
Board (Index Information Ltd): Prod=2206/188($89E/$BC) (@$200000 8meg)
Avail report:
Type Available In-Use Maximum Largest
chip 1923416 169640 2093056 1915112
fast 275878000 29246352 305124352 233832416
total 277801416 29415992 307217408 233832416