I bought the digital download version of the game from TGN, and a friend of mine bought the retail version in the store. We both updated to the most recent version of the game via stardock, and tried to play in a multiplayer match. When we tried to join the other person's game, we would get a message that the game files didn't match. We both tried a complete reinstall from our respective mediums, and the same problem occurred. The working solution was for my friend to uninstall the game, and install via digital download from stardock, without using his CD.
I don't know if anybody else has encountered this problem, but I figured I would throw it out there so that people know about it.
Our computers are, for the most part, identical. Asus X38 motherboard, Geforce 8800 GTS, 4 GB of RAM, Vista 64-bit edition.