I had the same problem with winUAE crashing all the time a few months back. Cant remember what I did to fix it though. although I think I ended moving the CPU Idle to the right a bit & disabling USB mode & now have no problems.
BTW im emulating 040 AGA 2MB Chip 8MB Fast 128MB Z3 32MB RTG. Runs 1200x800 32bit OS3.9 Workbench with Sound & everything :-D
