For some reason, sometimes the window focus is not set although rift thinks it has actually changed it, meaning I can resize the new focused window, center it, etc using the shortcuts. but according to the OS, the active app is still the old one, so any keybind will be sent to that app. Focus is only updated properly if I click the window with the mouse.

I also use an external program to draw a border on the current active window which makes the issue more obvious.
Unfortunately I have not been able to figure out what causes this issues, but it defintely happens quite often.
The solution for now is to kill all the open apps and restart rift.