We had a lot of magic flags on items. And quite frankly, little rhyme or reason to it. This has changed, as follows:
Magic flags on weapons are largely unchanged, as this reflects, or determines, whether a weapon is enchanted, is not enchanted, or can be enchanted.
Most magic flags on non-weapon items have been removed. Only items that give a magical affection of some type to the wearer have retained (or gained) a magic flag. This, for the most part, means: affects the wearer with some type of spell.
I might have missed some newer items in this change; if you see anything you don't like, feel doesn't fit with the above outlined rules, etc., send me a game mail.