I've recently updated to Xcode 5.1.1, and the cmd+R shortcut no longer works. Going into Preferences I see there is a conflict, but "Run" seems to conflict with "Run...". It doesn't allow me to delete either one of them, and changing one automatically changes the other one, leaving it in a conflicted state. I also can't find a restore defaults option. (This is in fact the "Default" setting, and I haven't customized anything previously.)
I suspect that this is a bug, but does anyone know of a way to get it working? (along the lines of editing or deleting some file)