I used a lot of graphic mods (skin, logos, faces, kits, etc), but I don't think those can actually affect FMM's database-related stuff - I've been using them for years without any problems whatsoever. Changes.txt too for license fixes, but they simply change names for clubs and competitions.
All of the problems I mentioned are database-related. As of 15.1.1, most of these hadn't even been fixed yet.