It is not unusual for pups to be picky and like a clean place to do their business. I noticed that while Rylie won't refuse to go on a dirty pad she will carefully place herself to not go where she has before. In addition, she does have her limits. 3 pees and she will not continue to go and I have to change the pad after every poop (which I do anyway 1. she used to like to pick it up/eat it so I wanted to get it right away, pineapple is helping with that, and 2. I don't want it to smell up the room!).
I think the two pad suggestion is a good idea.