Yeah, no problem. I bought the CD through Scholastic, a company that sells various things to teachers and students. I got Civ3, PTW, and Conquests all three together (but not the complete pack).
The game is version 1.00 when I install it and everything seems to work fine. It's never asked for the CD when I start the game (at least in conquests, original Civ3 and PTW did ask for the CD, but not conquests).
Scholastic is an official company, not some weird company selling illegal knock-offs. The only thing I could think of that would account for it being different is if they got custom games from Infogrames. I've emailed them and just haven't heard back yet.
I just about to get too sick of it all and return the game to Scholastic and go buy the complete pack from Walmart....