I suggest to create a backup and then deleting the GFX.ini in the Config folder. There's at least one graphics option that you can get somehow, that is not changeable through the GUI:
https://bugs.dolphin-emu.org/issues/10917
If enabling "Immediately Present XFB" or "Enable Progressive Scan" fixes the problem, your problem might be exactly the problem from the report.
If you don't care about 100% accurate graphics emulation, i recommend enabling "Immediately Present XFB" anyways, since it might display things earlier. And for performance, i recommend setting the texture cache to fast. If a game requires a slower texture cache setting, Dolphin should overwrite your setting automatically.
https://bugs.dolphin-emu.org/issues/10917
If enabling "Immediately Present XFB" or "Enable Progressive Scan" fixes the problem, your problem might be exactly the problem from the report.
If you don't care about 100% accurate graphics emulation, i recommend enabling "Immediately Present XFB" anyways, since it might display things earlier. And for performance, i recommend setting the texture cache to fast. If a game requires a slower texture cache setting, Dolphin should overwrite your setting automatically.