On my first crafting class to hit 20 I put the meld materia button in the second position of the second action bar. Now when I switch classes I have seemingly randomly that position changes to meld materia replacing what was in that location.

I think it happens for equipment sets near the bottom of my list as I never had it happen to my main in position #1 but it is somewhat random (or a pattern I haven't noticed) so it may be chance that it hasn't effected that slot.