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Those look like remnants, areas of the screen that are not getting updated or redrawn. It's symptomatic of resource starvation, your processor or ram memory is getting maxed out and to keep the ball in the air your kernel is looking at the redraw call and intermittently saying... " Eh, screw it".
If you run an htop, you'll probably see you are deep, deep, deep into swap (we've all been there, it's a bad place).
Try shutting down some browser windows (browsers suck up dynamic memory, chrome is the worst but firefox isn't much better). You could also minimize the browser or move it to a desktop not visible on the display (you're drawing a lot of layers here.).
Not to say any of that would help, but it's worth trying before giving up on Adobe Reader (which is no slouch at consuming precious resources either) and switching to Evince.
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