We have had this problem ourselves. It ended up being an issue with the map services, not the Flex viewer. Initially it happened when the rest cache wasn't cleared after a change to the services, meaning that the Flex Viewer was attempting to retrieve fields that were now hidden.
This happened in another instance relating to changes in the map services but I can't recall what was changed. I can investigate with the team and get back to you. Hopefully that'll give you a starting point at least, knowing that we did resolve the problem here