Not sure if they ever fixed this issue in subsequent updates (I'm still on 10.2.4) but if you're still having problems with screen sets when using the floating transport display/Control Bar (FTD), position may have something to do with the bug.
When I first solved the issue on my system I was using the FTD on my second display at the BOTTOM of the screen below the Mixer. Everything worked as expected until I decided to move the FTD to the TOP of the page. After moving the FTD's to the top of the screen my screen sets were messed up again.
Since moving the FTD's on my 2nd and 3rd displays back to the BOTTOM of the screen under the Mixer and Piano Roll (respectively) everything works as expected again, no problems with my screen sets.