Whenever I start CIV up and click on window instead of fullscreen (prefrences), the game takes up the whole desktop like so,
http://s5.photobucket.com/albums/y187/Starkow/?action=view&current=Thissucks.jpg
I go to options and change everything back to defaults but it doesn't work. How can I make it a window again?

The Preferences do nothing. Hold down the Command key when you launch and you can select Widow mode and resolution in the initial dialog. Alternatively, use the Options screen in-game. Select Graphics, disable Full Screen and choose your window size there.

That's exactly what I've been doing and it still does it.

I think that you have a window that is the same size as your monitor, and that doesn't really work. Try the next size down. I usually have not been able to select the same size as the monitor, but I have on some occasions, I don't know the pattern, though.

Not sure if this is related but starting with Warlords, I believe that if I hide the game or opt-TAB it, when I come back to it, there are graphical screwups (flashes and what not) until i quit and restart the game...

Anyone else?

What hardware? (CPU, graphics, memory ...)

What hardware? (CPU, graphics, memory ...)

It's a 2.66 Mac Pro, Nvidia 7300, 2GB RAM...

Same as mine, then.

The Nvidia 7300 has known issues with Civ4 and Warlords. I've identified problems with black terrain, and terrain showing through the fog, and the trees are planted at sea level. So it doesn't surprise me that there are other problems as you describe. I haven't seen them myself, as I run in windowed mode, and don't bother hiding it - I don't even play it much :p

It's probably a good idea to notify Aspyr, as I'm pretty sure they are working to resolve the Nvidia issues, given that it's the stock GPU for Mac Pros.

I see this also on my 7600 GT card in my iMac. I'm not sure that cmd-tab is what always starts it, but thinking back on it that could always be involved. I haven't seen it on any of my ATI video cards.