[jcarucci]

I think I've figured out the problem. This afternoon when I got home from work, I was careful to first press the sync button on the Omnifocus on my iPhone to get all the latest items on the MobileMe server. Then I opened Omnifocus on the mac and pressed the sync button. This time everything was perfectly in sync.

I think what was happening before is that I started the Omnifocus on my Mac and on the iPhone at the same time. Does Omnifocus have trouble merging changes from two different devices at the same time?