Bump: And I did some more testing on this. It seems to be the most evident when playing on large 1 - 2 star Custom made maps. If I play any of the stock ones or create a small map I don't seem to see the issue. Also it doesn't always present itself early I tried one game where it didn't start happening till about 30min into the game.
Once it does happen though that game will always be affected by it.
[UPDATE] Ok I made a map to force the issue. Two identical Star system, with a group of 50 Colonizable planets and 25 Uncolonizable planets, and with two players per system. The Interesting think of note I found was that when I previewed the map and Zoomed in on one faction the icons bounced all over the place, but if I zoomed into the faction opposite but in the same system the icons remained fine. This went the same for the other system as well, once factions icons would bounce around the others would not.
Also zooming isn't the only thing that can trigger this, If you hold the [ALT] key down to see health bars and pan the camera in random direction you will see the overlays on the ships (health bar and icons) shake when the camera passes certain points.
Anyone else seeing this issue, any Mod want to help us out?