Just a couple of problems to report so far:
(Should probably note that I don't normally run the game in windowed mode, had to change to it so I could take screenshots as printscreen was only producing black when using fullscreen mode)
Files:
- debug.err
- dxdiag.txt
- Game Save
[Bugs/Graphics] Reverse Video
First, there seems to be a problem where blocks of the map (both cloth map and zoomed in detail map) suddenly go into reverse-video mode. These blocks are clearly-defined squares and, when zoomed in, only reverse the landscape and not things on it such as units, buildings, and map items like trees. The effect only seems to last for one turn, but does come back at seemingly random times.

Here you can see the reversed video on the landscape and how it doesn't affect the detail items on the landscape. (Slightly unrelated: I'm playing as a custom Imperial Faction with a predefined Sovereign (red borders, Empire checked with Wraith citizens) and my revived landscape is oddly pretty and green. The AI Imperial faction nearby has the nice craggy desert landscape on his city.)

This is the same region on the cloth map. Note that the affected area is defined by the cloth map's grids. This wasn't the only spot to have this happen, and I'm not sure what defines the area it happens to.
[Bugs/Gameplay] Negative Population
The reverse video bug is odd but doesn't effect gameplay, while this bug pretty much shuts gameplay down. Playing as an Imperial faction, I had two cities and a population of between 10 and 20 (I'm not sure what it was when the bug occurred, could have been several turns after I had last glanced.) I suddenly noticed that I could not recruit any units anywhere, the problem being a lack of population. Glance in the corner and I see that my Empire now boasts a whopping population of -247 citizens.
My guess is that the problem is either from the fact that they are Death Worshiping and I built a sacrificial altar OR from the fact that I had recently researched the Slave Trading tech (it was the last thing I remember doing before I noticed the bug). Here is a nice picture to show the massive growth my capital city experienced because of this:
So I removed the altar, passed a couple of turns and then did a little fishing around
Found exactly what I expected to find:

An insanely large number!
[Bugs/Interface] Text Display
I figured I'd throw this in here while I'm making a post, but it's not a big deal:

Just some minor text display problems on the empire screen. (possibly elsewhere, but I can't remember where else I saw it)
Finally, the ability to load a saved game also seems to rely slightly on chance. The rule is if I click a save and then click Load, if the screen stays there then the game has crashed, if it changes to display the world name and "Loading World" or whatever then I'm good.