I've noticed a strange issue for a while now where if the mouseover 'magnify' effect is applied, triggering it causes various program windows to flicker. I can't figure out common factors, since it happens somewhat inconsistently regardless of mouse speed and program focus. I saw this post from over a decade ago that sounded similar:
https://forums.winstep.net/phpBB2/viewtopic.php?f=2&t=2938&p=8650&hilit=magnify+flicker#p8650
However, changing dock transparency had no effect.

That sounds like a video driver or hardware issue, sorry. Especially if it is intermittent.

What are your system specs (Windows version, GPU, CPU) ?

Also, whenever we're talking about visual artifacts a video uploaded to Youtube or some other media repository site is always welcome.

For some reason I can't recreate it for a video right now, but I'm running Windows 10 Pro (Build 19045) with a Ryzen 7 2700 and GeForce GTX 1080.

Okay, finally caught one in the wild. Here's a video showcasing it happening with the dock settings window:
https://youtu.be/W8X0VmQjNvc

Thanks for the video. That actually looks like a video driver/Windows issue, sorry.

Notice that the dock itself does not flicker. It is up to the Windows DWM (Desktop Windows Manager) to fully compose the desktop image before sending it to the screen, so that issues like that do not happen.

Oh well, at least it's not constant. Hopefully whatever is causing it gets patched at some point. I have to wonder if any AMD users have experienced something similar.

Sorry for dragging this post up from the grave, just thought I'd throw my expertise into the ring in case anyone else has this issue.

In addition to the obvious windows/graphics driver update possibility there's usually 2 main causes for this sort of thing.

1. Lower end GPU (or built in graphics) with only 2 gigs or less video ram that is being pushed to it's limit.

or

2. A lot of customization elements. Any combination of things that requires a lot of different elements to be rendered by different programs at the same time.

Windows will prioritize rendering "in focus" elements over background ones so if you're using an onboard or low end GPU and/or have a lot of custom desktop elements/effects it will cause windows to delay rendering the background for a fraction of a second to make sure it gets the in focus element right.

Actually there's a 3rd thing I've found that can throw a wrench in the works. If you run a lot of gadgets (rainmeter, xgadgets, 8gadgetpack etc) that are monitoring the system (drives, cpu, gpu, temperatures, ram, processes etc etc) it will mess up a lot of things on even a good machine because those type of gadgets are often set to check every second, so every single second there's 10 or 20 requests hitting the system for info which delays the CPU from processing other tasks.

It can make almost anything choppy, especially games etc. Trick there is to adjust the monitors to have different refresh times, so instead of all updating every one second, have 1 or 2 do it every second, then set non essential stuff to update every 2 - 4 seconds so it's not all trying to update at the exact same time.

Ah, that would probably be it then since I'm also running Rainmeter and a few Stardock apps. Granted I haven't tested for the bug without them but it's already inconsistent enough.

I think whmxtra may have a point here. If you watch the video frame by frame on Youtube (by pausing the video and then pressing the '.' key) you'll notice that the 'flicker' is actually the Windows DWM failing to render/show the Preferences screen.

It's as if something fails when the DWM is putting together all the different screen elements to compose the final desktop image - as a result, the flicker is caused by the background wallpaper showing through where the Preferences window should be.

A lack of available video memory could cause this, for instance.

Yep, I actually just watched the video, missed that link the first time.

That is 100% too many screen elements trying to render so windows is prioritizing the area where your mouse is and leaving the background till last, so it doesn't have enough time to render it on every refresh and starts skipping the out of focus stuff.

This isn't an AMD or Nexus issue, I have both Nexus Ultimate and an AMD processor. Now granted I have a 6 GB GPU so it's not generally an issue for me which suggests you either have less video ram than you need or you have too many rainmeter skins loaded. My money is on rainmeter

Even with a 6 gig GPU I can duplicate the issue somewhat (although not as badly). Loading a bunch of rainmeter skins, even static ones, causes a bottleneck between the CPU and the GPU because rainmeter refreshes like mad and windows is forced to prioritize where your mouse is and skip some other things. Especially if you use some rainmeter gadget skins for monitoring the system as the default refresh time on those is usually 1000ms and you have to edit the skins manually usually to change them as a lot of them don't have it built into whatever settings menu there is (if there is one at all lol). I use a bunch of them myself but I have all the refresh times staggered to make sure it doesn't mess with anything.

It's possible start11 is playing a part in that too, I haven't used it in ages and even then it was only in use for a week or so and can't remember if I had any issues with it or not (well other than not finding it particularly useful for my purposes hehe).

I think I have an old copy of it around somewhere, might throw it on here just to see if it makes the problem worse or not.

Best advice, either use less skins or adjust some of them, particularly any that show system info like drives, cpu, temperatures, ram etc. Set them to different times if you can, 2 seconds (2000ms) for things like cpu and temperature stuff and drive/ram/other non critical stuff can be set to 3 or 4 seconds. That should ease the bottleneck a bit and eliminate the issue.

Or you can test more by turning off 1 thing at a time (eg turn off start11, test, then start unloading 1 rainmeter skin at a time till the problem goes away and then you'll know exactly what is causing it).

With my setup I haven't had any issues and I have 2 docks + 5 drawers I'm using plus about 10 rainmeter skins loaded, plus a couple of older 8gadgetpack gadgets, plus sidebar diagnostics plus about 6 background apps running at all times.

Only way I could duplicate your issue was to load up an extra 20 skins or so at their default settings, then it started bottlenecking a bit.