Hi Erikari,
after an hour or two of fiddling around we found the solution. The problem:
first of all, we packed all our art in a single sprite atlas, with a scale of .66. After that, our artist used that texture atlas and unpacked it in every spine project to get all the art...but this is scaled wrongly and gave a mismatch with some art.
Because all of the spine projects were already made, we fixed it by repacking an unpacked atlas with scale 1, resulting in proper rendering. Strange though that it renders completely fine in spine, and not with the runtime, this had us confused for a while