I have got two major problems with zeta, first was when starting the quest, when i went to crashed alien ship, game stuck at the transition when i should have lifted into the spaceship, game started some animation and and then came back, but i could not move and could not use pitboy.
This was pretty much identical problem which i had also when i had a transition into Tranquility Lane, when i sat on the pod some animation started and then animation stopped and i was still in the pod and unable to use pitboy.
I had to use console command to move to the spaceship and start the quest.
Then there are a few missing meshes, robotic assembly and waste disposal seem to have a few.
Other major problem was when ending the quest, the teleport to wasteland did not work and had similar problem, it started some animation and then came back, and i was still in the ship, after that also the teleport to the engineering core stopped reacting.
The quest "galaxy ain't big enough" ended immediately after the spaceship was destroyed, but the final objective "Defeat attacking alien ship" was not marked as completed.
Using Fallout 3 Game of the year disc. 64 bit windows 7 with 16 mb ram.
Mod load order is the same as in installation page, tried without any additional mods from a clean save but did not help.
are the problems that i have had on my playtrough on whole game so far and all are related to transitions with some animation.