Doug,
After you have reset FLDIGI to the configuration you want. Run the following from the menu:
File->Config Scripts->Generate
Save the file to the location of preference. This file can be used to restore the set up when fldigi.prefs' and 'fldigi_def.xml get corrupted.
This method can also be used to configure FLDIGI to a particular set-up on a given event requirement. Just generate a baseline script file so the set up can be restored to "normal" FLDIGI operation.
Robert