My first guess at this would be that it is a Win 10 issue with the latest creators update if you updated to that. Are all the applications that have issues java based?
First thing I would try is setting the application to win 7 compatibility mode.
I tried win 7 compatibility mode, it made no difference to the display.
On my previous pc running the same OS and software with the same monitors but connected via DVI cables these applications had no problems.
One of the applications with problem is definitely java based, the other looks likely it is using java in the client.
Is there some issue known about java in regard to this?
Some further testing - I connected my main monitor (which is one that has the blacked out popups) via DVI. This shifted my main monitor over to other still connected via hdmi - that screen now gets the blacked out popups, the original one is now fine.
The problem seems to follow the 'main' (number 1) monitor.
So back to original config, two hdmi monitors -> added third monitor via DVI cable. Third monitor displays fine, the other two hdmi monitors now get blacked out popups. Don't know if this gives any other clues...
Can this relate to Radeon drivers or the way it interacts with the OS?
Open to all other ideas please
In case anyone else experiences this I just fixed it today.
Radeon software said there was driver update (17.6.2) and once I had that installed, I used 'clean install', then no more black windows.