I'm sorry you're where you're at :/ I looked at your profile and your scores were impressive.
Transferring graduate schools in the US is pretty much impossible and all-but unheard of. I'm trying to do it now, and I also got rejected across the board by everywhere I applied to. My scores weren't as good as yours, but I also didn't apply to just-top-20 schools. It hurts, though, man.
Yes, the very fact that you started your PhD at one school and then went to another school will count against you.
This might actually explain the reason for your rejections. In the US, people usually enter the PhD program immediately after a bachelor's degree. If you are applying with a masters, then you look like you're bailing out, and bailing out is bad on applications.
You would probably be better off doing paid research somewhere for a year or two, than doing the PhD program at your school.