Another 'me too' I'm afraid, favourites are still listed in the Bookmarks menu, but have disappeared from the bookmarks bar. I am syncing using the iDisk preference in OmniWeb.

Me too. My favorites were lost a few weeks ago, both in the toolbar, and then later from the menu. It happened just after my computer was forced by the network to change its hostname (quick disconnect and reconnect, and the DHCP server hadn't realized I was gone), which screwed up all sorts of syncing. Then within the past two days, the rest of my bookmarks disappeared. This is the first time in 8 years that OmniWeb has lost my bookmarks, and I'm not happy. I can rescue most of them from another computer, fortunately, but I know that if I start OmniWeb on that computer while it has an Internet connection, those bookmarks will disappear too - happened when I tried to rescue my Favorites.