Eye-patch lady only appears in DOTM, COTBS and TRF. So far, every other episode, although that pattern looks likely to break with the next episode.
She doesn't appear in TDW, presumably because it's outside of our universe.
As for why Amy hasn't mentioned it;
In DOTM I understood the implication to be that the heavy presence of Silents discombobulated her, never mind what they did to her underground. I think it's unlikely she remembers.
In COTBS there was a lot of weird stuff going on, and at least one other female apparition. If Amy doesn't remember from DOTM then she has no reason to think it's not part of the ship's medical system.
In TRF she didn't have a chance to mention it privately to the Doctor.
She may well mention it soon, especially if she associates eye-patch lady's appearance in TRF with her appearance in COTBS.