I had similar issues with the Flurry screen saver on my 5,1 with a GTX 680 ever since Sierra first was released.
When I upgraded from El Capitan, I started experiencing random desktop drawing issues. Screen saver (Flurry) would at random times be slow and choppy. Then the desktop would randomly freeze. Say I'd walk away from the computer for a few minutes, come back, click on a Dock icon to bring up an open app, and halfway through the "genie" popup visual effect, everything would freeze. Mouse would move but can't click or do anything. About 7 seconds later, everything would suddenly "catch up" to what I clicked or moved during the time it was frozen.
It kept doing this off and on at seemingly random times. I didn't think much of it and kept upgrading the OS for each subsequent release, thinking "maybe it'll be fixed now." Kept doing it. I would keep Console open on the errors/faults page and watch it to see what was happening to the machine whenever the random lockup happened. It was a sort of desktop compositing or graphical error (wish I saved screenshots of it) that after some time, would start repeating the error but then incrementing by 1. It would get to 999 or close to it and then at that point it would do the freezing up.
I wiped and reinstalled the OS a couple times. No problem at all for a few days then it would start up again. I uninstalled and reinstalled the Nvidia 680 drivers. Eventually I just stuck with the OS X drivers, and it still kept doing it. The machine was still usable but this issue was somewhat aggravating.
When 10.12.3 dropped, it still was happening. Finally the last thing I tried was the only thing I never did think about, the only commonality between El Capitan and Sierra was that I stuck with the same screen saver. I changed Flurry to one of the "less taxing" photo slideshow ones. Never had the problem since. Not once!
I can only guess that in some way, some sort of "timing subsystem" or whatever the heck that is somehow tied together with screen redrawing/compositing has some kind of issue with whatever graphical crap the Flurry and Arabesque screen savers use. Maybe something to do with how Metal is used to draw the screen with Sierra now? Who knows.
