So the problem isn’t actually related to gnome/mate. It is the program Vivado that shows up as black. I tried disabling client side hardware acceleration but it did not help. It is very strange to me that when I open the same session on my Windows computer, I can see Vivado just clearly. Vivado is a java app.
Actually as I try again today, I can see it just fine. I have restarted my computer since, maybe the hardware client side settings to disable them didn’t apply until I rebooted? Not sure, but it seems to work fine now.