Programs become unclickeable

I am running the latest version of premiere, after effects and audacity (also other programs in the suite but these are the ones where I've had the problem). I am using two screens, and at random the main window of the program I am running becomes unclickable. Instead it registeres as if I clicked right throug the window, and on anything located underneath. In the past I could solve this by moving it back and forth with windows key + shift + arrow key, but it seems this doesn't work anymore. 

I have not been able to find anyone else asking about this issue, so I might just be supremely unlucky, but any ideas would be appreciated.