I'm sorry for the trouble this is causing - we'll probably need more information to figure out what's going on here, and I'm not sure that info is going to be particularly forum-friendly.
Can I ask you to try the following, and email the results to email@example.com
so the support ninjas can help?
Open Terminal.app (in your Utilities folder). Quit OmniFocus, if it is running.
Paste this command into the window:
defaults write com.omnigroup.OmniFocus XMLFileManagerDebug -bool true
Next, open Console.app (in the same folder as Terminal.app), start OmniFocus, and try a sync.
We'll get a lot more debug information written to the console window. Can you send it to us?
You can then disable the sync logging by entering this command:
defaults write com.omnigroup.OmniFocus XMLFileManagerDebug -bool false