I don't know if this has been resolved, but I stumbled upon it in my own struggles and maybe I'll save someone else some headaches.
I had the same problem and it was because bitcoin.conf was not being read by bitcoin-qt. I had a command line option "--data-dir" to store the database on a different drive for space constraints. When you use this option, bitcoin-qt expects to find the bitcoin.conf in this data directory also. So the one in %AppData%\Roaming\Bitcoin is ignored. Therefore a port isn't actually listening.