The male Flameback is the dominant fish in the tank, and he's not rubbing nearly as often as you describe (I only see him do it one or two times a day, if he does it that day at all), so maybe he's marking territory. The mouth rubbing happens far more often since he started it, but I'm beginning to think it's part of some weird ritual he adopted ever since I rearranged the rockwork to remove a troublesome Sunshine Peacock. He only does it in one little cave area, and the rubbing is paired with him turning in circles, shaking his fins, and biting at nothing. I'd say this was a breeding thing, but there are never any females around when he does it. The female Flameback who was rubbing did it far more often (I saw her doing it 5 or so times a day), but only in the fry tank, and she's not doing it anymore now that she's returned to the 50 gallon. The fry I saw doing it only did it once, and I'm wondering if that's a dominance thing too, because the same fry immediately started chasing several others as soon as he was done. I'm assuming that particular fry is probably a dominant male. I'll keep an eye on the fish, and if it spreads to others, or if it increases or other signs of illness appear, I'll treat immediately.
As for the female, she stayed with her fry for about 3 weeks before I returned her to the main tank because I don't like stripping and she kept shoveling the fry into her mouth anytime I tried to remove her before then. She ate greedily during her time there, so that would explain that.
Thanks for all the help!