Web Deploy 3.0: Web deployment task failed. (Root element is missing.)

I had started a thread in General Troubleshooting, but there has not been any answers yet, so I've decided to start a new here. Here is my problem description:

http://forums.iis.net/t/1192976.aspx/1?Web+Deploy+3+0+Web+deployment+task+failed+Root+element+is+missing

In a nutshell it seems WD3 is not working when I have more than one Azure instances but WD2 is. My question is, are there any WD3 options to get it works again?