When positioning a skeleton at runtime, you are positioning the 0,0 world position. The 0,0 world position does not change when the skeleton data is scaled, but the bones that have been moved away from 0,0 of course do change position. How is your skeleton positioned in Spine?
You can use Import Data
in Spine and specify a scale, which is equivalent to scaling the data when loading it at runtime. This will allow you to see what is happening in Spine when you scale the data.