This sounds a lot like a bug which is scheduled to be fixed in 1.7, <bug://bugs/46136> (completed items from iCal sync are re-appearing in Inbox, but disappear upon clean-up).
I don't think we'll need your database, but it might be helpful to get some information from your debug logs. Our support ninjas can tell you exactly what we need and how to find it: contact them at
omnifocus@omnigroup.com.