[Brian]

Sorry for the confusion here!

When you say they "Won't go into their projects", do you mean that they end up in the Inbox after you synch? What happens if you hit "Clean Up" (Command-K)? Are the items successfully filed?

If not, when you open up the "Data" pane of OmniFocus' preferences, does the "Clean up should process items which have" setting match the actions you're having trouble with?