Before you get crazy about it - first we should try to find out if the reason is the 'CPAE'* bug.
The second idea: If you are often testing many different setups, a virtual PC might be the perfect solution; install, backup the harddisk file, check out... Some even support temporary disk operations which are discarded when the emulator closes, if I remember right. BOCHS is a free solution, but maybe a bit slow, I'm afraid?
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* CPAE: "Codec Packs Are Evil"
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