It's Civ IV Complete Edition (Vanilla, Warlords and BtS)
Of course, it is odd that you don't have this issue with 003 but do in 005 - can't think of any reason for that, but I want to rule out something simple first until we get a larger sampling when more folks try out 005. (Note: NZ and I cannot reproduce your issue)
I used to have a DD version from D2D of Complete, but can't remember the folder structure - it was a bit odd from their original versions (I owned separately and then they switch to Complete). I had disks before that and now use the Steam. I don't have the Gamersgate version but assume it is similar to D2D's.
I recommend doing the Vista fix thing again. So do the following (and I know you've probably done all this before):
1) Uninstall 005
2) Run Civ IV vanilla once..just in case you have never run vanilla before
3) At the highest level folder (Firaxis or Civ IV Complete or whatever), give Full Control to all users under Security. Also, uncheck the "Read-Only" check box. (all under Properties ofc)
4) Do the same for the Documents/My Games/Civ IV Complete or whatever (vanilla, warlords and BTS may have separate folders there..not sure)
5) Install 005 using "run as administrator" privilege
6) make sure your BTS executable is set to "run as administrator", which you probably already do