persistence profile and two vip

Assuming I understand your setup right (Nice diagram BTW), you want to put your persistence on the second (App VS) BigIP. Persistence is to keep you hitting the same backend. So on the proxy, it doesn't make sense. As it looks like the proxy only hits the 1 app VS.

I don't really understand why you need so many layers, but I won't try to understand that here.

Check what you're persisting on. It may be that you're persisting at the app VS on the source IP. And you'll only be seeing 2 of them (1 for each proxy server).