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I have the same problem (although I don't use an iPhone). On first try Omnifocus manages to write its file to the WebDAV server without any error messages (if the file doesn't already exist), but every subsequent try leads to the error message "Your database couldn't be synchronized, because the database on the server appears to be totally unrelated to the local database". This occurs even if I try to resynchronize without having made any changes at all.

The only useful error message I could find in the logs is
"Error Content-Type doesn't have two components (mime-type; charset)"
But I have no idea what that means...

I'm running the 17th July sneaky peek. My WebDAV server doesn't run on a standard port, but that doesn't appear to be the problem (since connecting to the server doesn't seem to be an issue).