As KEW said, they weren't duplicates as the values were different. Even if they were identical, I don't think it would be abnormal. It's just an AVR so I highly doubt they have enough build in intelligence in the algorithm to tell, and warn you that you have already entered the same values.
By the way, have you tried copying the PEQ settings from YPAO auto setup? I am curious to the values. As mentioned before, do it manually can be tricky. I wouldn't do it without using software like REW to see what's going on in terms of "before" and "after". If I were to do it blind, I would start by copying the settings from auto setup, and go from there, with slight adjustment and go by ears, but I won't do it blind anyway.