After a lot of reading about the systemd config files, I discovered that there's a seperate config file handling what to do with the processes when logging in. This file is called "logind.conf". All the parameters are dashed out with the standard for RemoveIPC to yes (man logind.conf).
After enabling this parameter and set it to "NO" (also changed the "KillUserProcess" to no) everything seems to work like expected.
Did several reboots, did the same process as before (opening rt_xtt etc.) and everything keeps working: hooray!!
I think I can call this a solution for now
Claes was right again, only the place where to change (probably because the way systemd works changes very much).