I have unlocked armor enhance and the second type of grenade, and my custom class already has them equipped, but when I visit the equipment customization screen, the armor enhance is still greyed out, as is the grenade. I think my unlocks aren't being saved if I don't equip them to a custom class. Is this a sort of bug? I don't want to waste my level-ups by unlocking the same thing several times over.

and i have this problem

Yeah, me too.
At all unlocks, not just weapons.
Suit-unlocks too.