Did you actually "Scale" the shoulder bone?

When bones are "Linked".... Never scale.... (It transfers Negative Scale!).... It's cause problems, as you see.
This is One Way to give the shoulder bones the correct length.
Select the Mesh and "Turn Off Skin" and "UNCHECK "Always Deform"

Unlink the Shoulder bone from the UpperArm bone.
Give the "Shoulder" and extra bone... you'll see why.Open Bone Tools
Select the Shoulder bone and click "Create End"

A bone is added...
Select the newly added bone.
Switch to "Local Coordinates"
Open "Bone Tools:
Click the "Edit Bone Mode" tab
Now move the
(NEW) bone to the correct place. (using Local coordinates)
Snap the bone pivots together:Select the upperarm bone.
Select the "Move" tool. (set coordinates to LOCAL).
Set "Toggle Snap" to PIVOT.
Click the tab to turn on "Snapping."

With the upperarm bone selected....
Turn on "Bone Edit Mode"
"Snap to Pivot" is set
Move the Upperarm bone to the (NEW) shoulder bone.

Link the upperarm to the shoulder

Select the Mesh and turn on skin and CHECK "Always Deform

The bone is now the correct length.
Skin is intact.
DONE.
Edited
6 Years Ago by
but0fc0ursee