Hi Mr Durian,
Sounds like my mod that you downloaded, sorry if I didn't see your posts over at the modding forum, but I don't visit it very often.
Obviously I take full responsibility for anything the mod might have done since I am its author, but I have not had reports of problems in general.
You say that you have Rome: Total War with no BI installed. However, you don't mention what version you have. I suspect that the problem is that you don't have vanilla v 1.5, which is the latest patch. Vanilla Balance Mod is compatible ONLY with RTW v1.5 (with or without BugFixer). I hoped this was clear from the install instructions but perhaps I could have included a more prominent warning.
Because the ununstall procedure for VBM restores RTW v1.5 files (rather than whatever you had originally), it wouldn't reverse the problem. Your best bet is to completely uninstall RTW, and then patch up to 1.5 if you wish to use VBM. If it's any consolation, your saved games should be completely unaffected and can be preserved.