Saw your post in my pursuit to fix this same problem, and I just figured it out. All you need to do is go into tools\manage emulators, highlight dolphin and go edit, and under default command line parameters, it should say -b -e, delete the -b. That will make it so dolphin launches with the game list behind as usual, or if you have it set to "render to main window" on dolphin like i do, the interface will be above the game window. No idea what -e does, but it works with that in place still, so no need to change it.