If you have Settings > Proxy > Use Hardware Encoder turned on, you should try turning that off. It may not be working on your system. It will not fix any existing proxies, however. You would need to regenerate them for existing files that have proxies. How you do that depends on your OS, but Settings > Proxy > Storage > Show… should open a folder showing them where you can delete them.
Not enough info. mkv can store all sort of things in many manner. Maybe it is affected by the known bug that was just fixed.