By default, uTorrent binds the uPnP address to the first network adapter it finds, which happens to be the Hamachi virtual adapter. So, DHT won't work through the firewall (and uTorrent performance is generally worse).
In uTorrent, Options->Advanced, set the net.bind_ip and net.outgoing_ip to the IP address that uTorrent should put in the firewall/router via uPnP (i.e. the IP address of the computer). Restart uTorrent, and everything's happy.