That's an odd one indeed.
Try the following:
1.) Delete the thorui folder within the EverQuest II\UI folder then re-launch the ThorUI AU and let it pull everything down fresh.
2.) Delete your characters "window placments file" in the EverQuest II directory and use one that I provide. (You can move windows around afterwards by unlocking all windows using ALT-O)
The window placements file should look something like servername_charactername_eq2_uisettings.ini