File check is random in that it usually just checks a handful of files (or the check system only checks for corruptions and most mods aren't corrupted), it rarely fixes issues from my experience.
I would honestly just re-install (back up your user folder though or you'll lose all your map / macro settings), it's not that painful with the new installer. I never use any mods now without xipivot anymore, since that allows you to just turn off every mod with a //lua u xipivot command.
Should always keep your FFXI install folders clean.
If you have high mip mapping with a lot of mods you're gonna have some problems. Honestly it's better to be selective with mods and not just install too many.