Not offended, just explaining my reasoning for suggesting stuff that seems trivial. Let's face it, TMTK is pretty wonky sometimes with regard to when it spits up on us. For instance, I'm always having to remake zip files any time I make even ONE change/addition to them, 'cause it tells me they're corrupt (even though they work fine in Windows).I did not at all intend to devaluate your suggestions. I actually tried if the things you suggested would fix the issue. From my former experience i just guessed it would not (and i've been right this time), but as the TMTK converter is just a black box, you might never know if things like varying texture sizes might not cause problems in certain edge cases - so it's always worth trying things like this.
As for the armature itself, i don't really have time to try more things at the moment. As previously stated, if there are errors in the armature setup and/or the animation itself, they are not obvious (at least not to me). It's weird that deleting the armature fixes an error which is usually traced back to invalid texture setups.