So sorry i cant be that helpful with whats going on but for some reason whenever i attach something in EVA like the connector port or strut the object it is attaching to gets pushed down a good bit. This on heavier craft can destroy the landing gear if its legs and breaks the wheels if its wheels which is obviously a problem.
if it doesn't destroy it then connecting it to another craft normally does.
If its a lighter craft it just jumps in the air then lands.
I can stop them from breaking by just turning off crash damage till i am done but yeah
my guess is its going to be a conflict with some mod, tho i dont really see how any of them could make that happen, tho some of them (lol a lot of them in fact) are "*outdated" aka haven't truely been updated for 1.4.3, but support 1.4.2 and or whatever
(edit) i updated intersteller extended to remove the warp plugin errors, here is the new log https://1drv.ms/u/s!Ah6sh_8mzN7BgTBy-0ApQH5eaXHf
could also just be that it doesn't like heavier craft, but im sure someone has connected it to much heavier stuff then i have, im just trying to make a little mining thing, well "Little" lol
i was thinking of getting the WorldStabilizer mod and seeing if that helped, tho it isnt when loading in so i dont know.
sorry again that i cant be all that helpful