Okay, so it is a well-known stock bug that Squad knows about and is trying (hopefully) to fix? That is good to know, thanks!
I'd like to add though, that the issue appears (mainly) on parts that is clipping, but since it only comes into play when two crafts are closer than 2.8-3.0 km, it seems unlikely that it is the clipping parts that is the problem. The problem would surely be more likely to be connected to the physics engine somehow glitching the graphics when it deals with two crafts at once? (if memory serves, crafts further away than 3.0 km is static models "on rails"). The fact that two crafts that are in close proximity when the game loads does not experience this bug (perhaps due to the physics engine starting the simulation on both simultaniously) would, at least to me, seem to support this.
