That's strange. I have two networked pc's at home, both running the same set of disks (including serial numbers) except for running the soviet disk in one and allied in the other.. and they network together just fine. My son and I play against each other all the time.
A problem we DID encounter was that they would not network together until each computer had logged onto westwoods internet servers and downloaded the patches into both machines.. then they networked fine.