It looks like your original input image was rotated to begin with (90 degrees to the side), and that during packing the atlas it has been rotated back by 90 degrees, making it look as if the original is upright. Part (4) in your screenshot shows that the resulting rotated attachment looks good, but the interesting part would be the orientation of the original input image. You mentioned 109 degrees, which confirms the theory above. Could you please have a look at the input images directory in your Spine project where all your attachments are, there you should find the original image.
If the original input image is showing the body part lying on the side (rotated 90 degrees to the right), it would be the easiest solution to use the same rotated input image orientation for consistency reasons and paint over it, instead of manually rotating some Sprite attachments after replacing them.
