Apologies for the issues with scale; I'm going to write an in-depth guide to what works and doesn't in regards to Unity's "excellent" hierarchy system.
The gist of it is though...
Don't scale the character. Just use FlipX - the SkeletonUtilityRoot will scale itself.
If you're using 2D or 3D colliders inside of the hierarchy, you shouldn't use FlipX or negative scale ever 🙁 Thats true for 3D model rigs as well. Especially if you're using physics joints and rigidbodies. My best suggestion is to instead rotate the character 180 about the Y axis in lieu of flipping.
Also, 2D colliders generally don't survive being rotated about the Y axis if they're part of a hierarchy... Sucks... Quite a number of Box2D users just accept this and keep 2 sets of colliders, one for left and one for right.
I've sent you a PM as well 🙂