everything looks pretty much the same on my system.  Can you post a screen shot?

It appears to be a problem with custom races; specifically, with ht update it appears to be that one of the ui colors you choose is used for some parts of the map. If the color you choose happens to be dark blue--like mine was--then it is really hard to tell that and the black background apart. I don't know of any solution for a game that has already been started, but for new games with custom colors, choose colors that stand out a bit against black. The Iridium, with a yellowy ui, don't have this problem when I start a new game with them.

I noticed that when I used a save game from the previous release I had the black starbases and anomalies...but when I started a new game the problem was gone.