Do you notice your game flashing black when you are loading into the main menu? Do you alt-tab while your game is loading in? Try not alt-tabbing.
From my knowledge, there's three main causes to this:
I) Your game starts at a different DirectX level and loads in a different one when the game fully loads in
II) Your game switches resolution when loading in.
III) You have conflicting graphics settings in your config versus VPK modules in your custom folder.
I) If you haven't refreshed in a while, I would get a new graphics config. Firstly, in any of these steps; make sure to check your autoexec.cfg (if you have one) or config.cfg. If you use Mastercomfig, double check that you followed the instructions for using an autoexec properly because it's different. You can try putting the DirectX level in your launch options:
-dxlevel 90 (or 80 / 81 if you use them instead).
You might need to put it in your config.cfg as well.
II) You can try the same above with resolution. I've had this issue when I used to frequently switch them back and forth. Just changing your resolution or aspect ratio can break the overlay. This problem is even more pronounced for Discord. Ideally, you use your native resolution and aspect ratio of your monitor. The command for your launch options is:
-w # -h #
Ex. -w 1920 -h 1080
III) Check that your config.cfg and autoexec.cfg don't have extra commands that effect your graphics settings that you've put in.
If none of these work you should also run Mumble and Steam in administrator mode to see if it persists. You can also put -safe in your launch options to launch the game in safe mode and see if it yet again, still happens.