No real help as such, and no answer as to why it's only taking shots of terrain, however I have struck a similar-ish problem myself with Civ4 not taking screenshots at all (having used the in-game facility successfully for around five years until recent weeks where Civ4 doesn't recognise my [Fn] key even though it works fine for non-Civ4 use) ...
... however a possible work-around may be; run the game in window mode rather than full-screen mode and take a screenshot from there. If Civ4's screenshot facility continues to fail, then maybe use another tool to take your screenshots (many graphics programs have a screen capture facility, and I've found the Snippet Tool from Windows 7 can also do the trick).
I hope this is of help as at least a temporary work-around until you get a more satisfactory resolution to the problem.
My only other guess - and it is a guess - is that you're using high-definition settings in your graphics options, and if you turned these down a notch you might get the results you're after. Given I've not struck this particular problem myself or recall reading of a solution from others, this suggestion is just a 'shot in the dark'.
