So nuke and repave had no effect. I uninstalled Java, and removed all versions of maptool and the .maptool folder from my hard disk, but nothing has changed.
You did restart your computer between removing and installing? That makes a difference.
If you really want a clean slate you can run the
Backup MapTool Registry Entries.bat
Remove MapTool Registry Entries.reg
files, in that order to clear MT registry info, but I don't think there is anything saved there. If you have default.theme in your MT root directory, you can rename it. This is the one I use. Just remove the .zip so it ends in .theme