We would need to know more about how you are setting animations at the skeleton, are all animations set on the same track?
Also, which version of Spine and which version of the spine-unity runtime (name of the unitypackage, also mentioned in the included version.txt
file) are you using?
Does the animation look correct and is only the SkeletonUtilityBone hierarchy wrong?
Apart from the above questions: it sounds a bit as if a key that is equal to the setup pose could have been removed by having Animation cleanup
enabled upon Skeleton export in the Spine Editor. Could you please check if this is the case and if disabling it fixes the issue?