i had this same problem when i first installed my orange box... i think thats where the root of the problem lies... i forget what i did that fixed it, but heres something that no ones yet suggested to try:
delete the game data from the games that arent working, which will force your steam to redownload all the data... that way, you arent getting it off the orange box cd's... which again, seems to be a possible issue... youre getting it directly from steam/valve...
just a thought
- RK