My problem, offcourse there was a problem, was that my square thumbnails would stretch the images. So annoying that I ditched the idea of square and went on with my day. Before doing so I did my share of debugging/googling forums, so I could rant to my co-workers afterwards. Mid-rant I realised what the problem was.

The thumbnails are set upon upload, so changes to the format is bound to make changes.
Solution: delete gallery and upload the images once more.

Lesson (re-)learned this time: When stuck with something it always helps talking with others about it.