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Almost certainly the sync is working properly if actions added on the desktop appear on the iPhone. It is important to remember that both devices need to sync for a change to be propagated from one to the other, because they don't pass the changes directly to each other, only to the central server, and simultaneously collect any new changes found there.

Add a new task to the Inbox on your iPhone. Sync the iPhone. When that sync has completed, sync the Mac. The new action should be in your Inbox at that point. If it isn't, open up the All Items perspective and have another look. I think you'll find it is there, but if not, contact the Omni support ninjas and have them take a look. 800-315-6664 or +1-206-523-4152, M-F 10-5 Seattle time.