As games get kind of long, the Empire Tree gets kind of buggy. Never seen this behavior except in Beta 2.
Normally I have my empire tree set so I only see things in the gravwell where I have something selected. As the game goes on, previous gravwells stop closing in the Empire Tree, so it gets very cluttered and I start to have a hard time finding things.
It is very odd, because it works correctly for a while...an hour+ sometimes, then it starts to go kind of haywire. Luckily it isn't a gamestopper, but it is very annoying.
You might be able to see the behavior in the replay I posted in my "Turtling!!" thread. In that game, you can see near the end of the game that my empire tree starts getting very cluttered. I generally play with nothing set to auto pin or "always show" in the empire tree.
Thanks!
Cykur