I'm going to go ahead and guess that both environments are within the same network and domain. If that's the case, outside testing another client besides your Wyse devices to help rule them out, it sounds like whatever is affecting your users is global across your environment. Try logging the traffic for a user that reliably has the problem, then check for anything interfering with the traffic. If you can get your network guys involved I imagine that would help.
Another thing I'd check into are the PCoIP logs, at the very least you should be able to get a disconnect code from your View Agents, but still check your broker and client logs too.