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What happens if you do a safe boot (hold the shift key)? If you only start up OmniFocus and then Mail, do you still have the unwanted keyboard shortcut?

To get rid of the file as I suggested, first quit System Preferences if you are running it. In the Finder, use Go->Go to Folder... to go to ~/Library/Preferences where you'll find the com.apple.universalaccess.plist file. Rename it to be com.apple.universalaccess.plist.keep and log out and back in again. This file keeps track of any keyboard shortcuts you set up, and removing it should give you a clean slate. You could also use the Restore Defaults button on the Keyboard Shortcuts page, though you might still want to keep the original in case you want to go back.