I have a longstanding issue with Application Shortcuts (ie. in System Preferences -> Keyboard -> Application Shortcuts). I can set up a new shortcut to a menu item of a specific application, eg. VoodooPad, and it shows up as expected, like so:
This works correctly in the application.
But every such shortcut I have ever set up later disappears -- I'm not sure exactly when, but at some point the prefs pane reverts to the defaults (ie. just one entry for 'Show Help Menu', and the newly-added shortcut no longer works.
Anyone have any idea why?