To turn on debug output, copy the following text and paste it into Terminal, and then press return.
Code:
defaults write com.omnigroup.OmniFocus XMLFileManagerDebug -bool true
Do that and then run a sync, and let us know what messages you're getting in the console. (Email it to
omnifocus@omnigroup.com and then post the ticket number from the auto-response email here in the forum, so I can find it, please.)