i had the same problem before... lvl 15 char, full int. i had an item with +3 int, which boosted my mag balance from 88% to 92%
i replaced it for another item with more defense but no blues, and my balance went back to 88%
(finally i decided to go for 92% and forget about a little more defense

)
If your balance was 95% when u unequiped it, u prolly had 95% before, not 96% (unless u changed armour or any other item which had some + int/str )
PS:
if u increase mag balance, phy one will go down (correct me if im wrong, but i think this happened to me b4)