In your second screenshot the bones appear in the same order on both the left and the right (bone11, bone10, bone9). I would have expected that you reordered them, why are they the same?
Spine should not lose the order of bones when you save and reopen. Can you please post or email your project so we can see the problem? contact@esotericsoftware.com We don't need any images, just the .spine file.
