Have you checked path order? (Filter > Fix Compatibility)
Have you added Enforce Compatibility Check to Font Info > Font > Custom Parameters, so you can use View > Show Master Compatibility?
If the outline changes a lot in one place (inflecting to non-inflecting), compatibility can be lost in TT conversion. In the most recent versions (1040 and later), you have to try pretty hard to trigger such a conversion error. Make sure you have the latest cutting edge version of Glyphs (Preferences > Updates).
Thank you very much for your quick answer! Actually, for a random reason I tried just to “cmd + R” my shapes and it worked… No idea why. Here is what the X looks like :