Make sure your installation is entirely tolowered. Save files, for instance, are created in upper case, IIRC.Bad luck; it still doesn't work ok in all cases.
For instance try to open EFF files. It will say it didn't find them. Or open a save game. Some of those internal files it will find, some it will not.
I didn't debug it.
I do not seem to be having problems opening EFFs. If it is not a case issue I am not sure what it could be, but maybe a little digging through the code is necessary. Are they biffed EFFs, or from the override, or both?