The way it appears to me is that through the transition of opening your marriage up to poly, your wife may have become more of a secondary to you instead of a primary. Whether it be because you genuinely don't feel the same way about her as you did before or because you are holding yourself back to stop any negative feelings that her other relationship may cause you to feel.
I have to agree that you aren't showing her as much courtesy as she showed you. She backed off when you were uncomfortable, and while it's not clear to me whether or not you told her it was okay to go back, she at least waited until things settled. Did she think you were going to react better the second time around? To me, it sounds like you two need to get some counseling/therapy to see if a professional can help you with the distancing issue and see what the two of you can do to reconnect.