After a few tests - Skyboxes appear to be broken; post 131111 beta.
I'm unable to determine exactly what is causing it though - the .glsl file which involves Skyboxes appears no different, nor does it have any issues when it explains anything about orientation. Not exactly sure where else to look.
Here's a breakdown:
Spoiler below!
In short, 131111 or beforehand has Skyboxes working just fine - and too, so does the layout which I constantly repost. The way the skyboxes appear when they are viewed in the Level Editor and Amnesia are just a repetition of the first image in the original basemap.
Opening the .dds I put together in Paint.Net also only shows the first image - but off memory, that is completely normal.
I also tried to make a skybox using a different basemap layout (vertical cross, to be exact), and had the same result, a repeated single side.