I've been playing around now, and Mopes' workaround does seem to do the trick. It's a bit annoying (and worth fixing, I would say!), but it doesn't make the game unplayable, in any sense.
Now you can call me a wimp for pausing all the time, but for any turn based strategy fan, this game is still quite excellent, so long as you can enter your orders and do your thinking while paused (but from this perspective, it becomes important to fix this bug).
For anyone reading afterwards, if the empire tree is mucked up, all you need to is to get the scroll bar positioned such that the object your interested in *would* be in the display, if it hadn't disappeared, and then click in the area of the empire tree display, and then the object will be correctly displayed (with all of it's child objects also correctly displayed). The higher the resolution you play at, the less painful this bug is.