@kazuma1992
Are you using Windows 7+? if not, this is the reason you can't use Citra, if yes, there are 3 points that proof you need to update your driver as I said first time.
You said you updated your driver, but according to your log, it's using OpenGL 3.3, if you updated driver success, it should using 4.1~4.4.
Then the second thing to proof your driver not work fine is you unchecked Hardware Render then Citra work.
And also many people play the game
Etrian Mystery Dungeon you tried without black screen, so your problem should not cause by Citra.
Although these points not 100% to proof your driver not work fine, but I think you should give it (update your driver) a try.
By the way, I think you should open your mind, instead always keep others' solution away when others want to help you. I believe you updated driver so I give you the second solution, I think you maybe knew how to change Graphic Card, so I told you post log, I also told you in this post, maybe is OS problem or driver and I'm not 100% right. Maybe this turn is time you should try my solution.