KSP is destroying my craft in the SPH

[MerlinsMaster]

Hey guys,

I've spent the last two days thinking I was going crazy, but now I know that I am not.  Here's a pic of a craft that I built:

 

Isn't it pretty?  Here's what it looked like after I left the SPH and returned to the SPH...

 

It's as if it is the victim of a transporter accident...

Is this a known bug?  

I'm running KSP 1.9.1.2788, with the most recent versions of both DLCs

I'm using Windows 10 64bit

Log file

Craft file

Save file

[Superfluous J]

I loaded your craft and it looks like picture 2 (broken) immediately.

My first thought is, how did you get them attached via those radial docking ports? I'm not asking this in awe I can think of at least 2 ways to do it I'm just wondering how you did it, as maybe that caused the problem. I know for a fact you can't just straight-up build something like this by taking parts and attaching them, you need to do some root-part doohickery at some point.

UPDATE:

I think you've found a bug, but I'm not 100% sure what the bug is yet.

I started with a fresh craft, simple just a fuel tank with radial jr ports, and was able to kind of recreate your problem.

[MerlinsMaster]

18 minutes ago, 5thHorseman said:

you need to do some root-part doohickery at some point

Yes, you're right.  I would bring in a subassembly that I had made, and before i place it I would use the rooting tool to select the docking port.  I suspected that maybe that might have something to do with it, but I've frequently used that method on 1.7.3 and had no problems.  In fact, I just went back to that install and tried replicating it, and the issue did not occur.