Happy to help out with this, but we're probably going to need to gather some information that's not going to fit well into a forum post. Can you do us a favor and send an email to the
support ninjas so we can help you that way?
One thing that would be helpful to include in the email - are you referring to OmniFocus itself syncing data onto your iDisk, or Apple's "Local iDisk Syncing" process?