It sounds like your JIT just isn't working...
I just tried AIBB on my WinUAE install (Athlon 1600+) - your machine should smoke this one.
Did an AIBB emutest with JIT enabled and it was waaaay faster than a real Amiga 4000 (scored about 250). Did the same without JIT and it was about 75% the speed of an A4000/040. Not surprising really, given that JIT is exactly what's needed for tight loops etc. (so don't go thinking that WinUAE with JIT or not is ever really 30 times the speed of an A4000 - it's not, unless your only use for WinUAE is to run benchmarks, anyway.
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Oh, I'm running Win2K Pro, 768MB RAM, latest version of WinUAE. Sounds like you have a software configuration problem somewhere....
