Bill, I had the same issue with SSB (LSB & USB getting inverted) with my scratch build. I don't like any software which does code changes magically, I like "Breaking the Magician's Code" maybe it just me. Don't get wrong the Memory Manager has it's own benefits, I would have taken a backup of the config before using the Memory Manager and doing any changes. I use the Memory manager to backup and restore my best tuned config and make another Arduino nano clone.
I think the best option will be to start with the CEC recommend factory reset and calibration process.