I was looking for this issue, and I see the OP hasn't followed up. I'm having the same problem--it doesn't go away later in the game, or with a new game. Using the lower or raise terrain spells seems to "fix" it in that particular area, but generally, if terrain displays as black it continues to display as black for me otherwise. I also seem to get area where adjacent terrain doesn't "fit right."

Also bears noting that I "can't" update my video drivers. I've tried to do so a handful of times in the years I've had this computer, and even the newest ones directly downloaded from Nvidia seem to degrade video performance, and give me weird graphical artifacts. I'm using the only stable version of my card's drivers that I've been able to find.

Here are two screenshots. Black terrain: Sometimes it happens over bigger stretches of land, but this was the easiest spot to grab a shot of.

And here's a shot of mismatched land:

Here's my debug.err: http://pastebin.ca/2006351 I notice it's also throwing out errors for things that haven't presented themselves in gameplay, such as fonts it can't find (haven't noticed any awkward-looking text while playing), and a few things in regards to my custom faction and leader.

Here's my current save file: http://www.admiraljoe.com/Ejolia.EleSav

My faction: http://www.admiraljoe.com/Faction_Ejolia.xml

And my leader: http://www.admiraljoe.com/Siyel_458018432-62508.xml

Edit: I just noticed,the debug.err is reporting the wrong version of Windows--I don't run XP Pro, I run XP media Center Edition.