My craft parts changes position when going to launchpad and back to assembly/ switching between VAB and SPH

[Dominik1]

Heres a video of it:

Any ideas how to avoid this?

[Vanamonde]

That is an odd glitch I have not seen before, but I have moved your thread to the support sub where someone else might have advice. Good luck.

[18Watt]

I see that sometimes when the root part is not a command module, probe core, or fuel tank.  Especially if I have used the re-root tool.

Try changing which part is the root to one of the large fuel tanks or the command module/probe core.