You can hard reset the menus by deleting a registry key:
Close PDF Annotator
On the Windows start menu, click "Run"
Type regedit.exe and click OK
Find this key:
For PDF Annotator 9.x: HKEY_CURRENT_USER\Software\GRAHL\PDFAnnotator\9.0\Toolbars
For PDF Annotator 8.x: HKEY_CURRENT_USER\Software\GRAHL\PDFAnnotator\8.0\Toolbars
Right click on the "Toolbars" node and select "Delete"