I would call Xerox and get a tech to upgrade your device. But there are caveats:
The newest firmware is a whole new version called "Connectkey 1.5" 072.010.104.14800
It is *highly* suggested that it is done as a "Forced Altboot, no data backup, no clone" which means an entire wipe, and set it back up manually as some settings just don't play well with the update. So the only thing that could be restored would be the address book, just export it, wait for the tech to finish, and then import it back onto the device. But everything else would be better if it was typed back in manually from a printed configuration sheet from before the reload.
I have seen reports of what you are seeing before, but not very often, typically it can be replicated if you very quickly scan to one location, and while that scan is running, quickly pick another and do another scan. What will happen is that even though you changed everything on the screen, it appears something in the back-end does not update quick enough and the repository does not change until *after* the scan goes through.
Any firmware this was seen on also showed an issue where if you pick a one-touch and select the "Clear-All" button you would see the scan defaults re-appear for a few seconds (Mostly only noticeable if you changed the default file name, you would see "Doc" briefly return.