I'm occasionally seeing the same behavior with a "Refresh on Logoff" pool, and if I watch the destop state in View Manager when it happens, the VM with the behavior does take a while before View recognizes that the user has logged off.
In one particular instance a VM was taking a really long time to show no user connected, so I opened a console window on the VM and saw that it was "Logging Off...", and eventually it really did. I still haven't found a reason why this intermittently happens (persona manager syncing, maybe?), or a solution, so if you come up with something please update the thread.
Geoff