A quick update:
Excuse me for taking so long to test things out, i have a lot of work to do at the moment so i have very little time for 3D-Printing.
My last few prints have been printed with the first extruder only, and so far the issue has not appeared again. I hope that helps a bit in diagnosing the issue, i will also try the new firmware next week when i have a little bit more time.
As a sidenote, thank you very much for the support so far, and for putting up with my slow testing 