Try deleting the following files:
Macintosh HD > Users > [i]yourusername[/i] > Library > Preferences > com.apple.logic.pro.cs.plist
Macintosh HD > Users > [i]yourusername[/i] > Library > Preferences > com.apple.logic.pro.LSSharedFileList.plist
Macintosh HD > Users > [i]yourusername[/i] > Library > Preferences > com.apple.logic.pro.plist
Make sure to backup your Key Commands before, as after deleting these files your Key Commands will be reset.