I've struggled with the DNS-323 and UPnP on both Media Player (10, 11, XP, Vista, 7) and also the Xbox 360...
Finally, tonight, seemed to make some headway...don't even know why I decided to mess with this as I had pretty much given up and used shared folders from the NAS to windows7 media player and shared from that to the Xbox. (The PC is on most of the time anyway since it acts as a DVR and servers media center to the xbox).
But anyway, if you save your DNS config settings, then reset them to default, then reload them it seems to fix the UPnP problems. It's very strange since you can reset and immediately reload them but hey, it works. I am now able to see the 323 in both media player and on the xbox.
See if it works for you.
If not, try to determine if there is a particular section of your files causing problems...basically the way you did already, by pointing at small chunks and verifying functionality. I've heard that a corrupted file can cause the UPnP scan to break and forks the whole process...you could have something like that going on.
Good luck.