Craig,
The most likely file that could be corrupted is sd.json in the data directory. It holds the actual settings for the program. Try renaming it, the program will make a new one when you reboot the Pi but it will revert to all default settings.
The file options.txt in the same directory holds the labels and tool tips for the options. It should be updated during a git pull. I tried renaming this file on my system but didn’t get what you describe.
Dan