So what you are saying is you already checked that this wasn't happening or have programmed around this problem.
Your posting implied that it was a single agent and not your entire group, hance checking that they weren't toggling the not ready key is a genreal issue.
Do you have anymore information.. are they recieving any calls at all from the skillset that you are marking as priority 1?
Is the agent on more than one Skillset Assignment and two supervisors have the priority set different. Thus the last supervisor to run their assignment gets the setting?
Have you checked to see if the call priority has changed bumping the call itself past the oldest call? Perhaps somewhere, in that or other scripts, you are changing the priority of certain calls queued to that skillset?
There are any number of combinations to cause something like that but if you are asking if there is a general problem that is fixed by a PEP of somekind I am not aware of any.