There are a couple different things that can cause the symptom you're observing - the thread was originally caused by a specific problem upgrading from OmniFocus 1.0.x -> 1.1; unless you're also upgrading from one of the earlier builds, there's likely a different cause that's causing the same error message.
If you have syncing turned on and you're syncing with MobileMe,
this may be the cause of what you're seeing. (If you're syncing via some other method, it would still be helpful if you included that in your email to the support ninjas.)
Once you contact the ninjas, we can definitely help you get this sorted out.