It's apparently a bug that you are getting that warning, judging from Ken's post in this thread: http://forums.omnigroup.com/showthread.php?t=14823
I don't know if this was never fixed, or if it was fixed and broke again, but you should use Contact Omni (under the gear menu) to send in a report that you are seeing this behavior. You can read the Omni support ninja's recommendations for what to do in that same thread, then if something bad happens, you're following their advice, not mine :)
I have Mobile Me, I have iDisk, I have a Mac, an iPhone and an iPad, and I have WiFi connection. Why the F.ck can't OmniFocus sync?