I have tested with

bmap_createpart
bmap_createblack
bmap_blitpart

with non square sizes , to try and duplicate your problem when you said it doesn't save non square skins .

but all of those saved them out , however they are filled with black to make them powers of 2, by the engine when applied as a texture skin , that's the only thing I can think of now ,that bears any kind of similarities with your problem , because I am stil not sure what functions your using so that I can try and duplicate the problem .

edit :
let me look in to this a bit more