Only issue with this theory is that they buildings are on the first turn before the Thalans could have built at the very least the Hyperoin Matrix.

The Thalans get the tech for all three of their projects as starting tech, so two of them could be built on the first turn (assuming they colonize a second planet on the first turn).

The player's turn comes LAST. This is only of major concern on the first turn, where you are seeing issues with one-off buildings being built before your turn even starts.

Every turn afterward, when you hit "turn", various things happen in sequence. Your ships on autopilot move, and any combat, colonization, etc. that movement causes is taken care of. Then, each AI civ takes its turn in sequence (not simultaneously).

After each AI has taken it's turn, your turn begins again. Income for the week is credited, then all building projects and ships under construction have their week's worth of production assigned. Then your research for the week is applied, then the game checks for culture flips. After this, you get the report on what happened, what got done, and are ready to give your orders for the turn.

In sequence, this is what happens during a "turn" and my reasoning for believing so:

1 - Income given, production calculated.

2 - Population growth added to colony

3 - Social building (I need further testing on these, it is possible 3-6 are in slightly different orders, but 4 will always follow 5).

4 - Ship building (possible that 2 and 3 are flipped, nearly impossible to check)

5 - Completed ships are created (this is treated differently from social projects. No matter what you do, you can only produce one ship per planet per turn. By rush buying you can complete two social projects per planet per turn).

6 - Research progress assigned (necessarily comes after social building, otherwise when you researched a  tile upgrade you would see one week of progress on planets that had nothing else in the queue - e.g. one week of progress on terraforming would be complete)

7 - Game checks for influence flips (I've never officially checked whether this comes before or after #6, but I asume after - shouldn't be hard to check with the fixed MCC)

8 - The part of the turn you can give orders, build stuff, etc.

9 - Ship movement and all activities related to that (set a ship to colonize a planet you don't yet have the tech for, but will finish in "one turn". The ship will hit the planet, complain it can't colonize, then when the turn finishes processing you can colonize it. I've lost planets because of this - someone else gets there between the time my ship fails to colonize and the next oportunity I get to move that ship). 

10 - End of your turn, each AI goes through same sequence of events.

*Sequence starts at #

Quite sure. If #3 and #6 were reversed, every planet you own (that wasn't building something else) would show one week of production on the habitat tile on the same turn you finished the research. Next time you finish researching something (anything, the same would hold true for any building that improves something you already have), look at the build queue for your planets (assuming autoupgrade is on). Each planet will show that the upgrade has been added to the queue, but no progress has been made on it.

Say you have habitat improvement nearly finished on Jan 1. You click turn, all your ships move and all the other crap goes on. While the turn is processing, you get the research screen and the prompt to choose another research topic (note that this prompt comes up at the beginning of the Jan 8 turn, not the end of the Jan 1 turn. The distinction is important.). Once you choose that, the turn finishes running and you get the list of things done, starting the control phase of the Jan 8 turn. Check your planets during the Jan 8 turn, they will show no progress on habitat improvement.

*edit*

What you may have seen is research completed due to finding a research anomaly. Such research would be completed during the end of the Jan 1 turn, which would add the improvement to the queue *before* the end of that turn, meaning the Jan 8 social spending would be applied to those improvements.

Willy, this is where your sequence has a slight flaw.

If you research Xeno Research and have a basic lab built normally during that turn, with auto-upgrade on, if you have both enough social to build the xeno lab and enough research to get xeno research that turn, you will start the next turn with a fully built xeno lab-not a basic lab.

Try it some time.

(Granted, this was in DA, where it was remotely possible to pull this off first turn.)

And it seems Hairless has seen something akin to that as well.

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TA testing:

In the scenario I'm testing, I have 61 social (enough to build a xeno lab) and a research lab in the build queue, which would give me enough research to put me over xeno research by 2-but xeno research doesn't finish researching, although the research lab finishes building.

If I rush buy the lab instead (to get me enough research to get xeno research in one turn, since it costs 50 instead of 20 now, meaning it's 21tp on very fast in a tiny), and set another one in the queue, and then turn my social down just enough to hit 59, the xeno lab is sitting in the queue after I hit turn with 1 production remaining on it.

If I turn my social down to 39 (1 less than needed for the research lab), it's still sitting in the queue as a xeno lab, with 39 production spent on it.

Therefore, research comes before social building.

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Additionally, 1 & 2 are flipped-pop growth occurs before income is given.

Oh, and pop growth does indeed definitely come before social building.  Thanks to recruiting center, this is simple enough to verify, albeit maddening.

So our order looks something like:

1) Pop growth
2) Income
3) Research
4) Ship building
5) Rush bought ships
6) Social building
?) Influence flips

OK I get it now, thanks all.  Seems kind of silly for those buildings to be Galactic Achievements when normally they can only be built by one race anyway.  It seems to only serve to mess up custom races.