You should have been clear from the beginning about what your problem was (.ini settings apparently not taking priority in SMS). Make sure you don't open the Graphics menu at all during gameplay. If that doesn't work, right-click SMS in Dolphin, go to Properties, and you'll see an Edit Config button somewhere in the window that pops up. This should take you to the .ini file associated with SMS. Make sure the [Video_Hacks] section looks something like this:
See if that works.
Code:
[Video_Hacks]
EFBToTextureEnable = False
EFBCopyEnable = TrueSee if that works.
