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Another possibility is that the preferences file is storing an "off-screen" window location. With OF running, do you see anything in its Window menu below the entry "Toggle Quick Entry Window"? If so, then you have an off-screen window.

You might try quitting OF, then deleting the file ~/Library/Preferences/com.omnigroup.OmniFocus.plist.

Relaunch OF and it will generate a new preferences file with default settings. (I'd recommend trying this even if you don't have an off-screen window.)