It's a really interesting situation, I think. I could imagine being like the OP--having found a place I'm comfortable, I don't want to disturb things, so I'll just quietly start paying the correct price and save $15 each time. I just wonder if I, personally, would be able to get over it, though--or if, like violetminnow says, I would keep thinking about it each time I went there.
I mean, the way I figure it, there's only a few scenarios.
1) The manicurist knows the OP has been paying way too much but never said anything to her, which is kind of dodgy. She should have double-checked with the OP right at the beginning, and not "assumed" it was a massive tip each time.
2) The manicurist has no idea how much the OP has been paying, due to the way payments are done at the business. That seems like a really bad way to run a business to me, especially one so heavily based on tips. How does the manicurist even know whether she's getting good tips from individual customers or not? What's the point of tipping if there's no connection between the money given and the job done? And, no one else at the whole business noticed, either.
3) Payment setup like #2, but someone at the business--not the manicurist--is taking advantage of the casual bookkeeping to skim from the till, so the records come out like they "should" in the end.
None of those things make me, personally, very comfortable. #2 is probably the "best" and it still suggests a really ridiculous level of sloppy business practices. I will be really curious about what happens the next time the OP goes there and pays only $20--if anyone even notices or says anything.