You should check to see what account they are using to log into the machine when at the physical console - if it's not the same domain account as used to authenticate to the View Connection Server then the session will not be seen as a match, and therefore the machine considered as in-use by a different user.
Also, it's worth double checking to make sure it really is the 5.3 agent installed on the machines - the earlier 5.x agent releases may not allow non-View sessions on the console to be mapped to the same View user in some circumstances.
Edit: I forgot to mention - when checking the user account, also double check that the session correctly shows up in the View Admin UI.
