hmm, running without startup-sequence, and setting for OCS, the pointer still is quite inaccurate, the pointer is in one place, and selecting aims at something quite further down from the pointer, using WinUAE. If anyone has any ideas... or I'll start a new thread so hopefully the emulator lot notice...
Try disabling the CPU caches too, it should work fine then. I don't know if it works fine with OS 3.5/3.9 SetPatch, so you can always try running it directly on bootup (no S-S directly on powerup).