This might not be relavent..
But my cat has a funny shaped ear (he escaped once and got in a fight and didn’t come home till his broken ear was partly healed)
And because of this his ear canal is smaller then normal, his ear builds up a lot of wax and it causes severe itching to a point thay he makes his ear bleed by scratching if we don’t get it cleaned out often enough
So maybe if that one perticular ear is hard to look in maybe it’s oddly shaped too and has built up wax or something
Besides that… hm. I found something that causes inflammation in the inner and middle ear caused by some sort of bacteria
Here you go:
http://m.petmd.com/rabbit/conditions/ears/c_rb_otitis_media_interna
This site has a lot of other symptoms. But maybe her ear isn’t inflamed because of the itching (you mentioned there was some inflammation assumed from the itching) but from some sort of bateria in the ear?
Hope you figure something out!