The iPhone sync doesn't want to work properly when using a port other than 80. I run apache on port 81 for webdav, and nginx on port 80 for all my other web services. When the iPhone tries to sync, it successfully talks to the DAV server on port 81, but then chokes on a "GET" command because it ignores the port I specified and tries to talk to my port 80 server.

I saw a similar post about OmniFocus for Mac having the same issue, but I think that was resolved in the latest sneaky peek as everything syncs perfectly fine from my desktop.