I'm afraid I'm not familiar with GM's skeleton_bone_state_set as that is an API they provide. My guess based on your description is that your call to that function and the internal animation state and skeleton update that GM performs are at odds. E.g. your call sets the bone transforms, then the animation state is applied by the GM Spine integration, which overwrites (parts) of your settings, resulting in flickering.
Since we do not have access to the GM Spine integration, I'm afraid I can't do much about this. Could you please bring this up on the Yoyo Games forums? They may be able to help.
