I don’t know if this is the problem, but I found another thread (here
http://forums.omnigroup.com/showthread.php?t=10870 ) that had this comment/suggestion from Brian at Omni:
“... if you shut down OmniFocus, then open up this folder
<your home folder>/Library/Preferences
and move the file named
com.omnigroup.OmniFocus.plist
to the desktop, does the OmniFocus window appear when you re-launch the app?”
I went to “<your home folder>/Library/Preferences” and I don’t see the file named “com.omnigroup.OmniFocus.plist”.