I suffered the same problem with Karmic Koala. I had tried unsuccessfully to 
install Pinnacle Studio 9 with Wine. I then wanted to clean up so finding that 
I couldn't clear the menu items with Alacarte I  uninstalled the Wine software 
and deleted the .wine directory in /home/user/. I still couldn't delete those 
menus.
I finally managed to remove the un-deletable menu entries which were now in the 
 "Other" menu group by going to /home/user/.local/share/applications and moving 
all the unwanted entries to a new folder (including the Wine folder) and then 
moved it to a different location, In my case the desktop. I only moved the 
files as a precaution, they can probably just be deleted.
I hope this is of use.

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Cannot delete some items
https://bugs.launchpad.net/bugs/268279
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