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I just tested this to see if it was a problem for me, too (I didn't want to make new projects just to see them disappear!).

Here's exactly what I did:

1. Made a new project on the iPhone
2. Hit the sync button on the iPhone (I didn't want to wait the 1 minute for it to self-initiate the sync).
3. Open OF on the desktop, wait for it to self-initiate the sync
4. Check to see if my new project was there. IT WAS.

Leo, are you sure that your iPhone synced with your server before you opened your desktop OF? That could be the cause of your problem.