Hope it's not a pirated version
Wine isn't perfect, I think their site says that. I've noticed too that if one version of Wine can run some program(s), it doesn't mean all newer versions can. Bugs are of course fixed all the time, but of course Wine is never going to be as all-around-working as a native Windows (not talking about the native Windows bugs here).
If you found a version of Wine that can run your program, stick to that. Don't fix a working thing - a thumb rule. And if there really is a Linux client for Doom 3, you should be using that and not running the Windows copy over Wine..