I got this screen-in-the-screen-thingy in MarioKart Wii since rev 3403.
It looks much better when i first choose "copy EFB to sytem RAM" and then turn it completly off.
But i don't get the results as perfect as it was before, there is still a black block, like before the hack was implemented
My save-file gets also corrupted everytime i restart dolphin
I used to have black bars. Try enabling the "Auto scale (try to remove borders)" option under graphics config. I also have problems with my MKW save. I just keep a copy of it in the root folder.