I have seen this problem across many servers and it has led to plenty of disagreement about where on a ship a partner is. Most recently seen on the cake server walking a friend through my build. Neither of us appeared in the correct place for the other person.

The gif (created using the built in gif creator, failed to upload to imgur... here are some screen shots instead.

As is normal, after finally submitting a broad bug report, I was able to track down the freeze to a SINGLE block. There is a rail in the shuttle bay control room (in the top portion of the head) where a single rail somehow became linked to two other rails. I will include a screenshot of the rail with one of the links showing as well as a shot of the logic sitting beneath the rails\buttons. Removing that one rail unfroze all blocks. Oddly, this one rail was linked even on blueprints from before I had a freezing issue. I suspect that the linking was a result of one of the rail updates in the last few months.

I have my enter\exit button set to R and still get sporadic rolls when exiting my ships.

I would like to note that, in contradiction to Kiithnaras's experience, I have had entities that were both spawned as docked, and manually docked come detached without any visible cause. Just today, I came back to a large build and found that I was getting around 5fps. Eventually, I discovered three separate entities un-docked from different parts of my build.

Just anted to make sure the link from T1130 was not lost. Imgur gallery illustrating the issue for NOT Gates and Flip Flops being used directly to affect rail changes: 4 states