Mac App Store shows pending update for update that was done
Here is what we found. And it's not a completely satisfactory answer, I'm afraid. We had installed some software called PowerBroker, to give individual users the ability to do tasks they would normally need admin permissions to do. (This would allow limited tasks, such as updating Acrobat or their printers, etc.)

This user, being a developer, was testing this out. We had actually uninstalled PowerBroker, but something was left behind that continued to cause problems.

We actually "fixed" this by installing PowerBroker 1.3.1. Even after we had removed it earlier, and even though it was not doing privilege elevation, this installation fixed the issue. We did a deep into the OS, and none of the logs were specific about this. Very frustrating. We do have cases open with PowerBroker about this as well.