you should go see an audiologist. for a cheap price, you get to know exactly what's happening instead of getting anxious from doubts(and it could be wax or a small rash on one hear).
in fact very few people have perfect balance at all frequencies, usually the lack of attention and the brain compensating like mad, let people unaware of the fact. the most affected are soldiers and hunters as the gunshots are always on the same side. but simply the difference in shape of both hear can be enough to change the sound a good deal even with no damage at all.
I don't know about the balance control of the iphone, but I suspect that the volume gets lower when activated(if only by the fact that you're lowering one side) so that would translate in "hearing" a sound of lesser quality (following the famous "louder is better" psycho acoustic effect). also if you're hearing imbalance is only for the top trebles, then maybe you find the iphone's balancing wrong because you correct high freqs and then notice the rest getting imbalanced?
if it's really a problem for you(go see the audiologist!!!), I can't say for an iphone EQ app, but at least on a computer you can get left and right EQ separated, so you could do a much better job compensating just for what you need where you need it, instead of just a balancing slider.
you send tones in one ear, try to EQ flat, do it for the other ear. repeat process a lot of times to be sure your result is about right => see if left and right have big differences => use left and right variation to EQ just for you. problem solved at least for a few years.
the weak point here is that when you'll change headphones, they will probably have some matter of imbalance themselves(several DB are not uncommon at all), so a setting for one headphone might not be perfect on the next one
did I mention that you should go see an audiologist first?