Yes, they are in a single chain one on top of the other.
It appears the server is completely ignoring the setting. It should have stopped me several times from docking then. I say that because you are correct that is in the config file.
MAX_CHAIN_DOCKING = 25 //maximal deepness of docking chains (may cause glitches depending on OS (path and filename length) at high numbers)

It still exists just checked in latest versions.
http://i.imgur.com/vXu9N1d.png
The stack you see on the left is what i created in game 128 docked entities.
The right was what came of trying to admin spawn a copy of it. 108
Figured that was faster than building an entire station and entities over again.
The system still thinks there should be docked parts on it and tries to transfer you up to it if you use the arrow keys. This results in a Long pointer null exception error.

Andy you are welcome.

The attached file is a zip of the logs from trying the new pre-build.
The first time entering the world I didn't even make it in before error occured.
I tried again. Upon doing so i got many many errors flashing across the screen and red text to small to see all across the screen. So i did some looking to see what I could find before the server shut down.
i took a screen shot of what I seen. I enclosed it in the file as well.
It probably would have been better if I recorded it.
From appearances the errors happened as the ships loaded in. It appears you created a function to test if a child entity is missing from the parent from looking at the error log.
I would bet this is a database race condition as I posted in the thread.

Just a quick question on this. I was considering putting in a potentially related bug issue. But it might not be depends on how your resolved this.
The bug I was going to report is if there is a long chain of entities docked such as I had station modules docked to a station with ships docked to that and other ships docked to that one and the turrets and so on.
Apparently that also will end up loosing entities.
It is different based on which OS you are on. It is related to the directory structure and windows only being able to handle certain length paths to files.
I realized the issue when I was making large chained power supplies. I didn't consider the issue how it might effect other stuff. Or there might be a circumstance someone docked that much together.
So that was a bad assumption on my part and I should have reported it then.
Anyway the question is this issue related and does the fix to this fix what I am talking about or does that need a separate report?

Ok, just wanted to update this.
Reloaded the server that didn't help.
Mongoon was the only faction listed with me attached to it saying own:
I decided to see what would happen if I simply created the old faction with the same name.
Well when I did that actually allowed me control back of the station and the faction block.
It now shows both factions on the faction list.

The current bug with the power being placed in rows doesn't change with the camera movement. The state of the blocks that won't allow placement doesn't change until I set a block on the nearest blocks to the ones that won't work.
In short I put down a row of 100+ another 100 blocks.
At about block 170 and above I can't attach anything else to them.
So I connect a block to 169. That triggers the system to look at what else is attached and initialize blocks 170 to 200.
I can now connect to the blocks 170 to 200. I can set it so that I am 1 block away from these blocks when I place them down and it still happens.

I'll see if I can give a better description. I put down the first row of 100 power blocks and move to extend that row. I put the second set of power blocks down and it places them you can see them. But if you try to connect another block to the end you can't it doesn't give you the build indicator box(yellow). Instead if you go down along the row of blocks flying beside it you will see some place around 70 for example the build block disappears. However. I found if you attach a block to that number 70 it will fix the remaining blocks as well. So what I end up doing is connecting a block on the side of the last one I can and remove it then go to the end and attach the next segment of blocks.

I set the block size you can set down at one time to being 100 length. I then set down 100 blocks attached to the core. I then set down a second set of 100. I ran along it checking with the yellow box to see if and where the blocks could be place about 20 or so blocks from the end the yellow box disappears and you can't connect any blocks to the power blocks that are visible.

Just tested it myself still exists in current version. If you need I can provide screen shots or video as proof.

Did some more testing on it and screen shot what was going on. http://imgur.com/a/3Bfvs
The next day I got back on a large section of the ship weapon system completely disappeared. http://imgur.com/a/lI3Ia
Worst bug I have ever seen in this game.

I took a ship to the shipyard that I had built outside of the shipyard it was fine before hand. I saved it. My purpose for using the shipyard was to get a more accurate block count by taking it apart and putting it back together. So I saved it to a different blue print when deconstructing. Upon reconstructing it everything looked fine. However I parked the ship and logged off and when I came back on noticed the turrets were floating around.

After using other blocks to get it to bring the cursor up. When placed more blocks on it. It says, "area not initialized yet please place blocks slower"

I'm was saying there is 50K storage their because you said there was none. "Your turrets do not have power storage on there own as far as i can see."

http://starmadedock.net/threads/block-count-is-off.21446/
You can find the ship here. And image proving the count is off before saving. Second ship worse. off 12%.

First, off you are dead wrong on the turrets not having 50K storage. Anything with a core has 50K. You can verify it the way I just did. Put a single power supply on the turret and what it charge 50K. Take it off it doesn't go down 50K. Now fire the turret and it will show it being 50K less.
Coincidentally you end up with same out of power again which still get while firing.

The station in referred to is this one http://starmadedock.net/threads/pirate-barn.21348/