Whenever I send my avatar through the automatic avatar setup it sets up the avatar facing the wrong direction, but the arm bones are flipped, which is weird. Kind of seems like it knows the left from right hands but gets confused on everything else
We recently added “Manually align front” as a setting to toggle for Avatar Setup, which will set the negative Z axis as the front view of the input avatar. Please have a try to see if this fixes your issue! Feel free to file another bug report if you run into any other issues.