It is magical, except when it isn't :-)
I wonder if your preferences file has gotten corrupted. Quit OmniFocus. In the Finder, do Go->Go to Folder... and enter ~/Library/Preferences then click the Go button. Now find the com.omnigroup.OmniFocus.plist file and rename it to something else and relaunch OmniFocus. See if the undesired behavior persists. If it doesn't, mail the corrupted file to
omnifocus@omnigroup.com and ask them to figure out what went wrong. You'll need to re-enter any of your preferences that you changed.
If it doesn't do the trick, then you might as well move the old one back and contact Omni support directly.