I've done quite a bit of web searching and have not found anyone addressing this specific issue.
After upgrading to Sierra (macOS 10.12.2) the Application Switcher (horizontal popup with app icons that pops up when you type command-tab) is noticeably slower.
One of the reasons it is slower is the graphics draw times.
When it initially displays it paints from top to bottom. The painting is so slow it is easy to see its progress (maybe it takes .3-.5 seconds). Then when you release the tab key it redraws again with lighter colors then disappears.
Another problem I have is that the Chrome (even the Canary version) Hangouts extension is completely unusable because draws/refreshes are slow or repeat too often. Those redraws occur as a series of rectangular areas around the window. Each rectangle draw is slow enough to be visible. Another Chrome symptom is that the tabs for each open web site flash incessantly. This all happens with hardware acceleration disabled in Chrome settings.
The Hangouts bug is the important problem since it is the only way I know of to get Mac notifications for instant messages through Google.
My hardware is a late 2010 Mac Mini with an NVIDIA GeForce 320M 256 MB graphics chip and a single monitor connected via a digital cable.
Also, I upgraded from an old version of macOS to Sierra, skipping at least two versions (Yosemite and El Capitan I guess).
The same 'slow draw' problem occurs in Safari when I open the attach file browser from Gmail.
Best Answer
It turns out that, somehow, the graphics chip was no longer recognized by the OS when these problems started. The flashing and flickering was apparently due to the slow processing of fade-in and fade-out animations when these animations were rendered by software instead of hardware.
I know this because I downloaded Maxon Cinebench and it told me my graphics card was "Apple Software Renderer." When I rebooted the graphics card then showed as "NVIDIA GeForce 320M OpenGL Engine."
I don't know why the OS did not recognize the Nvidia graphics chip but I assume it will happen again which would give me a clue what caused it.