GLKTexture is not correctly mapped since iOS6

You should report the bug to bugreport.apple.com as already mentioned. As an aside, if you are suggesting that GLKTextureLoader is maybe the problem (seems like a good theory) then you might narrow things down in one of two ways off the top of my head...

1) I would render the texture shown to a trivial quad and see if the render results are what you expect., i.e., is it rendering vertically flipped from what you expect? Is the source texture partially garbled in some way that you weren't expecting?

2) You could try converting your image to a different size/color depth/image type and see if the problem still exists. What I'm thinking is, and it seems unlikely, but maybe it's not being reported because you are hitting an unusual edge case due to something with the image format. Knowing this would be of huge help to anyone trying to fix this at apple.

Probably not much help but without having access to all your source and assets, pretty hard to know what to suggest. FWIW, I have some samples that do similar things to what you are doing and haven't noticed anything under GLKit v. 10.8.