I deleted the prefs.ini file and it did improve things dramatically. The dithering still remains though but now it looks smoother.
Before the update to Beta 3, the map icons were (or seemed) crisply solid with no softness applied to them which to me looked like that tactical map was a computer display. Which was fitting for the game. Kind of how the displays in Star Trek TNG were bright colors with crisp solid edges.
Now there seems to be a filter applied over them which does not look bad per say but it dosn't look as 'computery' to me - it will just take some getting used to.
Here is a better example I am talking about. Notice the relic icon and how it is all softened. I am playing at a 1680x1050 resolution. This screenshot is at the same scale as I see it in the game. Also notice the terran icons are all 'smudgy'.