It does happens from time to time, but there's no easy way to track, check or test.
First, I would double and triple check the Call Presentation Class.
Second, check the login/logout report and verify that against the agent performance report.
If nothing stands out from the above check, rebuild the phone. After all of this and it's still a problem, it's tracing time on the AACC.
Just my .02, but more than half of the time when this happens, it's the agent causing the problem. What I sometime do is go to the phone and make sure the agent is watching and reboot/reset the phone and I tell the agent I just updated the phone with keylogging so I will know exactly what button is being pushed and when. Surprisingly enough, the problem usually goes away after this.