Sorry for two posts in series, but I did try to replicate it somehow myself right now, at least to make sure it happens on my PC constantly.
Now I was able to do it with "[b]Skylone[/b]" built-in ship [b]as well[/b].
So I created a bookmark with F6. Then closed my SE.
Then I started SE, F6 -> Go to the below described bookmark -> Build a Skylone ship -> Take control ->
Start randomly firing the engines (main/reverse/hover) ON (to some 60-90%) and OFF (to 0%) with the [b]keyboard[/b] (Numpad "+", Shift + Numpad "+", Ctls + Numpad "+"). Just towards the Earth as ship is spawned, no camera moving, no HUD changing, nothing.
And one moment one of them stops respoding, to both keyboard (no response at all) and mouse (there is a change of power level, but goes to initial state immediately).
My log this time (in case required) - https://pastebin.com/EvibFd1C
The bookmark code
Date "2018.08.28 17:38:53.75"
Pos (-000000000000000000001F6C98CA6393 -000000000000000000000DA019A7DB90 +000000000000000000004AACCBFAAD4E)
Rot (0.6616682691767558 0.1672849384874971 -0.7060582843296994 0.1889247205880478)