Please always state the version and not just "latest". Now, while I am no fortune teller to know any details not provided about your ROM like CRC or MD5, I just went the general route and played my ROM versions, one of them being the largest X3 hack there is. They work absolutely perfect for me in 5.0.0.
As SaulFabre also mentioned, you should also always check against a previous version, preferably as far as the game starts working (in case it really is the app). This is the safest way to ensure it is an emulator problem and not just corruption on your used media, which may happen from time to time.