I have a simple setup, where the ninja's body is one SkeletonAnimation and the hands are a separate one using a BoneFollower. When the ninja flips using FlipX, the hands appear to flip upside down for a single frame before behaving correctly again. The BoneFollower uses followBoneRotation and followSkeletonFlip (I hadn't updated the runtime to receive the followLocalScale addition, but I just tried and that didn't change anything), and this behavior occurs both when the hands are a child to the body and when they're not.
VIDEO
(Situation in the clip used for visibility purposes, but it happens in all situations no matter what)
Interestingly, when viewing it frame by frame, it looks like the hands are flipped upside down for one frame BEFORE the body actually flips, and next frame once the body flips, the hands are correct again. I noticed that the hands transform's y localScale is set to -1 when flipped, so the upside down part makes sense, but why is it being flipped before the body is? Just an unfortunate effect of script execution order?
Using Spine 3.4.02, Unity 5.3.4p6, last updated the runtime September 13th it looks like...