Not for sure, but I think you need to turn off Cliff of Dovers "auto-update" in Steam if your running the TF-Mod. Cause everytime Steam updates and checks the CoD files, it see the Mod as bad files and over writes them......
Someone can correct me if I'm wrong, but that is most likely why your CoD stopped working....
Steam will autoupdate COD to the last developers patch. Once you have the Team Fusion patch installed over the Steam install, Steam will not automatically overwrite the TF patch, unless you ask Steam to verify your install.