Lostpacket - I'm really sorry for the trouble this is causing, and myself or one of the other support ninjas will be happy to investigate this.
We're going to need to collect some information from the phone and your sync server that isn't very forum-post-friendly, though, so can you send email to
omnifocus-iphone@omnigroup.com with a link to this forum thread?
There's a problem that could cause something similar to what you're describing, but we'll need more info to determine if that's actually what you're seeing.
If this is the problem I'm thinking of, the iPhone application may have added those transactions to the database in a way that isn't actually valid. In previous releases of the app, once that happened, it would break your ability to sync. (The current release of the Mac and iPhone apps prevent this from happening.)
If this is what's happened, the Mac app may be ignoring those transactions during the sync process. That said, we leave the transactions in the database specifically so we can fix problems like this by hand. There isn't a single fix that will work for everyone's database, which is why we don't have the app do it by itself.
Anyway, I'm not sure this is what you're seeing, but it's one possibility - if you contact us, we'll be able to get it sorted out.