As far as I know, Auto ISO was never designed to account for flash. It was designed to compensate for low ambient light when a specific minimum shutter speed is desired. So there is nothing to "fix" as it works as designed.
By trying to use flash with Auto ISO, you are attempting to do something that the camera is not designed to do. You are introducing another variable in the exposure that the camera cannot account for. If you see it "working" it is by accident, not design. (The onboard flash is pretty weak, so, depending on the scene, it may not be contributing more than a little fill, anyway.)
There have been many threads about this in the past, but people seem intent on ignoring the design limits of Auto-ISO and complain that it is broken.