Is it properly identified with at least one or two other programs?
If so maybe sysspeed doesn't understand the EC version and reverts to calling it a 68040. Much like the default WB 3.1 showconfig does with an 060.
Erroneous identification might account for the Mhz discrepancy too (i.e. standardised code that would be timed X running on an 040, which sysspeed believes it does, but is timed Y when running on the 060).
Just a shot in the dark as I've never run sysspeed.