May the issue be that these applications are restored before appmenu kded module (qdbusmenu) is set? If so, the solution would be to start qdbusmenu first and delay restoring applications until done.

I saw other bugs that could be related to this, although I am not entirely sure they refer to the same thing:

- https://bugs.kde.org/show_bug.cgi?id=384392 <-- I don't think my issue is application specific, but just happens to the applications first appearing (sometimes different windows of the same application behave differently just because some of them were restored before and some after)

- https://bugs.kde.org/show_bug.cgi?id=376728 <-- I think it's the same issue, at least according to https://bugs.kde.org/show_bug.cgi?id=376728#c5. 

What I'm proposing is an entirely different perspective given https://bugs.kde.org/show_bug.cgi?id=376728#c7 so that the issue is fixed by ksmserver instead of the globalmenu part of plasmashell...