having same problem here.
it's definitely the copy protection. my 2nd disk reads fine if i put it in first, otherwise every cd after the 1st looks like the 1st. it never updates until i reboot.
these copy protections squemes have been causing problems to legit customers for months/years, but companies still feel they are better screwing some legit customers to stop a few pirates. (only the noob ones, anyone who cares to do 10mins searching the web could figure out how to break it.)
sad, last Firaxis Game i'm sure i'll buy.
PS i didn't get a 3rd disk (manual disk?) that i saw mentioned on forums, but that's another issue.