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OK, I figured my problem out. A couple of weird issues.

I opened up synch preferences and noticed that my iDisk synching (no Me synching) lost its preferences and showed that I had never synched. I re-registered my computer. That created a second client instance of my Macbook, but whatever.

Once that was done, when I tried to quit, I got the window that says "OmniFocus will quit when finished synching". I initially clicked "Don't Quit" thinking that meant I'd be telling the app "OK, finish your synch and don't quit without synching". What it really means is "stop synching and don't quit". When I tried quiting again, I let the dialogue box sit for about 10 seconds and the app quit. I think the confusion part there is that there's a progress indicator bar that doesn't show any progress so you're kind of left thinking that the app is waiting for you to do something (hence, me clicking on "Don't Quit")