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I agree. This has been a major annoyance for me since I first tried 5.5. This is one of the reason why I don't keep OmniWeb as my default browser for long. I've emailed Omni about it and they're not sure of the cause of it either. For some reason they're unable to duplicate it even though it happens to me on two machines very consistently.

Supposedly moving the Favorites.html file from ~/Library/Application Support/OmniWeb from it's original destination, restarting OmniWeb, closing it, and moving the file back fixes it. Sometimes it works, but the problem just keeps coming right back for me.