Ever since Windows 10 updated to Version 1903 a couple of months ago, my front end has become very unstable. If I have two windows open, that blink back and forth from one to another and repeatedly update for up to a minute. This happens when I open the definition of a function, for example. The whole windows GUI is becomes unstable. One suggestion I found online was to disable the new memory control security features in Windows. That seemed to help for a while, but the problem has recurred.
IT DOES NOT sound like a Mathematica problem. Also “window flipping” is not a usual complaint for Windows 10 or Catalina either. What it is typical of is a “stuck or broken mouse, joystick, or keyboard”. So if you have a USB joystick and it’s on it’s side or broken - you might well get weird effects like that.
Before installing a new Mathematica always remove the old one (which is simply a few steps). Your user directory may contain “local values” and you can keep that (but it may cause issues - is not supposed to - will be re-created if deleted - if deleted will loose your local settings).
I agree it is clearly a Windows problem, and it turns out that installing Windows version 1909 cured it.