A reinstall fixed it. Or at least, saving preferences while running as Admin. With regular permissions, it still fails.
There is a fix that will allow updates to the file for regular users. It involes creating a new permission setting on the user.settings file, adding yourself as an authorized user with Full Control:
If there's no way to automatically set this permission on installation, have you considered using the Registry to store those variables? I've never tried it myself, but it shouldn't involve setting funky IO permissions when you're compiling.