FS-UAE can run WHDLoad without workbench, if you just after playing game.
Still, I am using WHDLoad with Classic WB Full in WinUAE and I don't have no issues like you.
Somewhere on board I posted changes to disable JIT/change to normal speed and return once WHDload exists...
Lookie here: http://eab.abime.net/showthread.php?t=24891
Paul covered that in his guides: http://guide.abime.net/wb3.1/miscwhd.htm