I've noticed that occasionally the buttons on the right hand side of the map get all screwy (i.e. placed behind the faction power listing) when certain things occur. In this example, I had everything turned on except the mini-map: Faction Power Window, City Hud, & Terrain Window. The UI placed the buttons behind the faction power window after I attacked and killed Magnar. I think there are other catalysts too - I'll post them here if I notice them again.

Zip (saves of turn before and after I killed Magnar, shots, debug) - http://dl.dropbox.com/u/19969679/Elemental/119m/UDFv0.1h/strategicuibuttonissue.zip

Here is right after I killed Magnar. Note the alert of Magnar's death is behind the faction powers (behind Yithril's FP of 4 you can see the skull flag). They were fine previously.

I turned off the terrain window and voila, it reset the UI layout. Note how they are now all visible.

I turned the terrain window back on, note no change. Certain catalysts, among them killing an AI player, seem to cause these buttons to do the Macarena. It's easy enough to reset it manually as a player but from a polish standpoint something to look at.