Sorry for the confusion this is/was causing! We've gotten occasional reports of this happening to folks in the last month or so. I got it to happen to me, as well, but only once.
The one time I did get it to happen, I had switched from OmniFocus to the iPod app on my phone mid-sync; the next time my Mac synced, it popped up this message. Couldn't get it to happen again, though. :-/
I captured the phone, mac, and server databases when this happened; from looking at them and the ones that customers have been willing to send in, most of the databases aren't actually incompatible when the alert comes up. (One person that contacted us did have incompatible databases, so the message was appropriate in that case.)
While we look into this, it would be helpful if folks (especially folks that have it happen repeatedly) contact the support ninjas
and let them know. That'll help us gather info and eventually solve the mystery.
(If you get the message and you aren't sure which version of your database has the most recent info, contact us and we can help there, too.)