Hi,
Today I've updated Web Deploy mudule to version 3 RTM by WPI in a Win 2008 R2. I've also updated my dev environment and installed Azure October 2012 SDK for VS 2012 (which also updates Web App Publishing Wizard as far as I know somehow).
The problem is Web App publishing is not working from now. I can publish my site once (per server restarts), but after the following publishes won't succeed and instead I've got the this error in the VS Error dialog window:
Web deployment task failed. (Root element is missing.)
There are no errors in my client machine's and server machine's Event Logs. It just ain't work.
I've tried publising to a Win 2012 server (WD3 installed), same error.