[whpalmer4]

Ah, you probably have MobileMe iDisk syncing turned on in your system preferences. OmniFocus talks directly to the MobileMe servers, whereas the rest of your computer (Finder and various apps) will write to a big disk image that is synced with the MobileMe servers on an hourly basis if you have that feature turned on. Unless you really, truly need it turned on, I would suggest you turn it off because there have been multiple reports of people having sync problems as long as it is on and vanishing once it is off. You would not see anything appear on your iDisk after OmniFocus did its initial sync until a MobileMe iDisk sync takes place, though the data would be there on the MobileMe servers and your iPhone or other OmniFocus desktop would be able to sync to it even though you can't see it yet in the Finder.

Another possibility is that you just aren't looking in the right place on your iDisk (the Documents folder) but I think the former is the likely explanation. I'm not aware of any reports where OmniFocus claims that it has synced with MobileMe and yet no data is actually written and no error message returned. You would see an "!" in the middle of your sync button or a little "i" in a circle in the Sync preferences panel if an error had occurred, and clicking on the little "i" in a circle would report the error again.