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Just a point of clarification: Lizard mentioned in another recent forum post that Bug 48521 referred to a different (albeit similar) sync problem that I've been having, and I'm not sure if you're tracking both problems on the same bug number, but I'm not sure if my sync issue has anything to do with the iPhone.

In a nutshel this is what is happening to me:

1. I edit my omnifocus database during the day on my work computer
2. before leaving I sync one final time to the server
3. I fire up omnifocus on my iPhone and see all of my most recent changes

then the trouble begins...

4. I arrive home and open up omnifocus on my home computer
5. it performs a sync but only some of the changes made on my work PC during the day sync back to my home computer
6. I open up my iPhone again and it is now displaying the incomplete database from my home computer (rather than the correct database that it showed before I left the office).

This may have something to do with the iPhone app, but it may not. So there could be more than one bug at issue here.