Well, some further tests shows, that this seems to be system related. Maybe there is something wrong in my Windows
On my work/gaming PC i have this error now even in the first Win64 build i was able to find: 2016-09-11.
All of them shows the same behavior. Single Missions are only visible alone.
But i found out, that all of them are shown after i have reclicked through the Single Missions button for all Single missions. But i was not able to fix the CTRL+SHIFT+S issue however.
The intesting part is... both builds works on my Gaming Laptop as they should in this terms. So that seems to be a problem on my side here. So i have to look for some recent changes in my system that were exclusive to my PC, because both systems uses the same OS and the same Anti-Virus that both got updates in the meantime.
But in the end it was a false bug report from my side. Sorry for that.