How is my user.config Settings file getting corrupted?

I've had a user send me in a crash report from a call to Settings.Upgrade():

System.Configuration.ConfigurationErrorsException: Root element is missing.

I got him to send me his user.config file and the file was all zeroes. It had gotten corrupt somehow.

I found a way to recover from it by rooting around the %localappdata%\MyAppName directory and deleting all user config files and re-launching the app. If I let the app continue execution it would give further ConfigurationErrorsExceptions.

Could this corruption be the result of something I've done? I've had multiple reports of it from a base of a few thousand users, but I have not been messing with that file directly. Has anyone else run into this user.config corruption?