My spine characters have their regular graphics, and then I also have a set of normal-maps that match the exact size of each of the original images - so its sort of a similar situation as yours.
There isn't any randomness to how the texture packer lays out the images in the atlas, so if everything is 'correct' you should end up with matching atlases, as you'd expect.
If you're 100% sure that you have the same number of images, and they are the exact same size (a single pixel difference can throw everything off), then the only things I can think to check are in the "Regions" section of the Texture Packer Settings:
1) Do you have "Alias" checked? Are there any images that might be duplicates, where Aliasing could be removing one from one of the color-sets but not the other? Try turning Aliasing off and see if it fixes it.
2) Do you have Strip Whitespace X/Y enabled? Try disabling it and see if that fixes it.
In fact, you know what I'd do is just un-check all 5 of the options in the "Regions" section, re-export your atlases and see if its fixed. If it is, then add those settings back in one at a time until you know which one is causing the issue.
If that doesn't work let me know I'll try to help further.
