I used speed hacks in some "heavy" games,
Despite the emulator claim to work on full Speed{50/60 FPS}
there is still a Slow down in some games,especially in "heavy" areas.
VU stealing does that in grandia 3 ffor example
if you use an old version the 3X cycle hack did that in almost every game^^
try using the latest beta pack (if you don't already) if it's still present after deactivating VU stealing try 1.5X cycle that has seemingly never this effect Oo
also see if it changes when you play windowed , fullscreen limited speed or normal Oo
as kabooz already stated, speed hacks cause that with some/many games. sometimes different combinations of speed hacks work better, but trial and error is usually the only way to find out, as it may also depend on your specific hardware. i believe bositman said that especially the combination of frameskipping (config->cpu) and vu cycle stealing/ee sync hack is prone to create such misleading fps values.
I don't use frameskipping
cause I have NEVER seen the fps actually increase XD maybe it's my hardware but IMHO frame skip is just a error possibility
Frameskipping in CPU options is not the same with VU Cycle Steal from Speedhacks.
As it has been said before, most likely the VU steal hack is causing the slowdown, disable it and test again.
ok, I did it and now even games like SOTC ans MGS3 are working almost full speed ^_^