Spine's export texture packing is different to the texture packer.
That is, if you use the export (ctrl + e) to create the atlas, it will obtain different results to if you use the texture packer (ctrl + p). The reason is the export - for what ever reason - doesn't take certain texture packer settings into account (such as combine subdirectories).
Depending on how you export your textures you will need to use the same .atlas file. I.e. if your textures come from Export use the .atlas generated from the export. If you generate your textures via Texture Packer, you will need to use TP's .atlas file.
I think you may be running into this problem. as clearly have rotation option clicked in one, but not the other. Even though you may have the same settings in both Export and TP, Export will ignore certain setting.
Hope this helps