This issue was resolved, in a less than comfortable way though. Today, the Queue went belly up. Apparently that part of the system just freaked out and hung causing lots of problems. Mostly switchboard related as we could still receive queue calls, just not transfer, or pause or any of the other queue operations. The rest of the system was normal. After a full reboot, the queue lockup was resolved and now the calls taken in the queue panel is correct. Apparently, it was something in the upgrade process to 5.5.3 that eventually caused the queue process to die. After working with support on it, they said to always make sure you do a full reboot after doing a point release upgrade just to make sure everything loads correctly.
Hope that tidbit helps someone else.