I tried replicating the issue with the same setup before sending, but was unable to reproduce the results. It may have been due to the sector boundary as you suggested.

Another odd picture:

I just tried to replicate the results, with two standalone ship cores, and got another unexpected result:

That's right. I directly jumped from one ship to another. Neither ship was docked to anything else. I can try it again and see if you need confirmation.

As a matter of fact, I am going to give you the very ship that has been experiencing this problem. The elevators near the ship core have a habit of becoming disconnected if the rails change direction while moving. The splitting door on the left side of the ship near the front have not successfully opened and closed once. There are some rails and spaces for doors to come down in the very front where the ship opens to the unenclosed area where I had previously put the same door in four locations and one of those locations did not work at all and one only worked on occasion. If the ship doesn't load or the file doesn't work, please let me know.