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.