I have the Deluxe retail box version of GalCiv and the expansion, but ran into a couple problems installing. I'm posting here in case someone else finds it useful.
My CD wasn't installing (aborting due to a bad setup.exe) so I used the stardock central app to download it. (Click create account to get it.)
However, the most important problem was that my key codes are reversed. I could only register the original with the code listed as the altarian prophecy code and vice versa. It took me ages to even try that, so hopefully this might help others.
I too had difficulty installing GalCiv Deluxe Edition. Ensure you have no virtual drives installed or screen savers running. Once I removed these, I had no problems with installing GalCiv.