So if you scale the mesh (using the scale attribute) and scale the joints the mesh is bound to, you'll get double transforms and the mesh will scale up twice as much as the skeleton. The proper way to do this is to scale only the skeleton.
What made be giving you trouble is the scaleCompensate behavior on joints. If you scale a parent joint it will not scale all the children with it. In the image below the top mesh has the first joint scaled up, and the bottom mesh has a transform node above the joint chain scaled up.

When I work I usually create a group above all the skin joints in a component and scale that, but the method for achieving uniform scale can vary from rig to rig.
Sorry I don't have a simple answer for you but hopefully that info will help you find the source of your problem.