Aha! you are scaling the entire group, armature AND mesh in one go I think. This is not necessary - just scale the armature and the mesh will follow, if you scale the mesh at the same time as you scale the armature, chaos ensues, since this scale is applied to the mesh on top of that already imparted to the mesh by scaling the armature, i.e. it is scaled twice - not good, the bones no longer fit the mesh. When you apply the scale to the armature, it is also applied to the mesh, since the mesh is a child of the armature. Hope this all makes sense.
Also you have some hidden armature layers, this could be a problem when you scale - not sure about this but…
Finally, I always scale an armature in Rest Position, not Pose Position - don’t know if this could also be a factor… It seems to affect the pose if I apply a scale to your model, having scaled it in Pose Position, the same does not apply if I scale it in Rest Position (you do not see this until you apply the scale BTW).