Reproduction Steps:

1. Open "MinimalRepro.zip" project
2. Open "SoldierFreeScene.zip" scene
3. "GameObject" -> "3D Object" -> "Ragdoll..."
4. Set some of the appropriate bones

Expected Result: The Bones are set in the Ragdoll
Actual Result: Sometimes the Bone being set, hovers over the slot until the mouse is moved
or gets pushed back to the hierarchy window when the mouse is moved

Reproduced with: 2017.3.0a3, 2017.2.0b6, 2017.1.0p3, 5.6.3f1, 5.5.4p2

Note:
Doesn't always reproduce. Seems to be partially random/partially how you add the bones to the slots