This is an update for users that may read this with similar problems:
I ran into slowdowns again the other night, so offline in steam wasn't the problem. I NOW believe the problem is PunkBuster, and I got it working again by manually updating Punkbuster via their website and the pbsetup utility.
This has now happened a few times where I join a server and its choppy, and the solution I've come to is choppiness= Punkbuster needs to be updated. If I close CoD4, update PB, restart, open CoD4 MP, it's fine. Don't know why restarting works but when I update PB and run CoD4 its still choppy. (And just restarting w/out updating doesn't work).
I still am not positive what the deal is as that seems to be a rather odd solution, but as I said earlier if you are reading this and having similar problems try the above.