The Dolphin versions I tested all had the exact same settings, including the same screen settings and everything else.
No other Wii game I tested has this problem in either version. The black bar is there the entire time, even on that warning screen. Also, if you compare the two images, you'll notice the part that's showing appears to be very slightly stretched. However, in anything after that, there's a big black bar that covers part of the actual game. In Dolphin 5.0-6081, everything looks normal and the game works fine.
Playing Resident Evil 4 Wii edition, NTSC USA, RB4E08. I'm experiencing a weird issue that I think might be a Dolphin bug.