Sorry mate, will try and clarify:
My pc came partitioned, i.e. my 150gig hard disk was split into a 40gig (HDD) C: drive and a 110gig (DATA) D: drive. The operating system (XP) and other essential programs and files are stored in the (HDD) C: drive, while music, films, games and other non-essential programs and files should be stored in the (DATA) D: drive.
I believe the reason for this is incase the need arises to reinstall your operating system (XP in my case) if/when something goes wrong; or if I wanted to install Vista without losing whatever I had on my pc when I was using XP.
So, when if I'm installing Civ4 etc, I change the place to save the game files from the default C:\Program Files\Firaxis Games etc, to D:\Program FIles\Firaxis Games etc.
The problem arises when the program you are installing, for whatever reason, doesn't let you change the location of where it is going to be installed. I think Civ4 and the expansions are guilty of this, or if they are not then the downloaded patches won't work unless the game is in C:\Program Files\Firaxis Games\ etc (which is why I've got half the game installed in one place and the full game installed in an other).
What you need to check is the pathway for BtS: to do this right click on the BtS icon on your desktop; properties and check where the game application is looking for the game on your pc. As I said in my previous post, the default location is "C:\Program Files\Firaxis Games\Sid Meier's Civilization 4\Beyond the Sword" but because not all of the game files were there (they were in my other, larger drive (DATA) D:) I had to manually change it in the icon properties to -> "D:\Program Files\Firaxis Games\Sid Meier's Civilization 4\Beyond the Sword\Civ4BeyondSword"
The main thing to remember is that the pathway in properties etc must be where all the relevant files for the are. So, after checking the pathway follow it yourself, so you click on My Computer; then whichever drive the pathway says, if it starts off with C:\ double click on that, then Program Files etc right through and make sure the files are there, if not you only have to copy and paste, or even easier change the pathway itself to wherever the files are on your pc.
I think this problem has more to do with the computer not finding all the files it is supposed to find and thats whats causing the problem, and what I've tried to describe above is how I fixed the problem myself.
So, try looking at the pathway first and make sure that where the computer is looking is where the files are!
Hopefully that is a little bit clearer - if not just say and I'll try again.
P.S. - The screenshot is what your screen should look like in the Beyond the Sword Folder, the only difference is the wee file with the planet in bewtween < > those arrows, thats because I have a program to edit xml, but everything else should look the same.