I've set up a test server running the latest version of 2012 and configured RemoteApps.
What appears to be happening is that after your initial logon to a remoteapp, when you close the session your user profile disk is staying "in use". So when you login again, if you get attached to a different VM (which seems to happen every time), then it can't attach to the UPD, so you get logged in with a TEMP profile.
Additionally, it seems like once you've had someone attach to all of the VMs, then you can no longer connect to any of them. They are basically one-use VMs. Once they've all been connected to and disconnected from, you get this error when trying to run any remoteapp:
There are no available computers in the pool
Looking at the server manager the VMs all say "disconnected" but they also show the last user to login under "user".
There aren't any errors or warnings in my event logs that seem related or are even from the specific times.
Rebooting the server fixed the issues only until users logged in again and it started over.
I'm at a loss, as this VDI/VM stuff is kind of new to me.