Im a Mac guy and Ive noticed it occasionally too.
Doesnt happen all the time, but once in awhile the menu will be greyed out.
EDIT: I just figured out how to do it I think..
Select File->Open and pick a game. (I used good old 10 Yard Fight)
Voila no options.
Theres actually more menu choices then I thought greyed out..
Options menu only selectable choice is Transfer Random Barcode
Edit Menu only Game Genie and DIP Switches.
File Menu only Open, Open Recent, and Page Setup. Not even Reset is highlighted.
However, if you open Nestopia, and use the Open Recent menu to open a game in the list, everything works as it should..
Any console log or something I can send in for help?