Well, WinUAE can be tricky to diagnose. However I would try using a vanilla AmigaOS3.9 bootfile. From your description of your setup it sounds as if the AmigaOS files are in a FAT32/NTFS folder? Try using a harddisk file instead. For my setup I placed all the AmigaOS specific files on a dedicated HD file. All my apps and data however are stuffed in a regular FAT32/NTFS folder so I can access them with Explorer, etc. I have found that there are cases where certain file names or file locks can cause problems when you are accessing a native Windows filesystem.
Aside from that I'm not sure what else to say. I can say that my setup has the CPU set to 68040, CPU emulation speed set to Fastest Possible, 8MB JIT cache, Const Jump, FPU support, Force Settings, No Flags and Indirect are all checked. It works fine for me.
I've also found that some badly behaved Amiga software can cause WinUAE to crash. Make sure you're not running any hacks. It's possible that AWeb causes problems, although my registered version works fine under WinUAE. There's also a "winuaeenforcer" that you run and it might help you find any misbehaving software. Anyway, good luck!
- Mike