I don't want to jinx it, but I've been using cafiine with custom music for a few days now and haven't banned yet. (Stay tuned on this, might release something to help with music replacement later.) I know of 3 other people (not including myself) who say they haven't been banned yet either. My current theory is that they validate the integrity of specific files (ex Static.pack because it contains things like weapon params), but not others.
If all the folders are there, then I'm not sure what's wrong. Perhaps try extracting all of the .pack files.