I think there's a problem with the Atlas maker. I have 3 pngs that fit in 2048 x 2048 (including paddings), but the Atlas Maker creates an Atlas of 2048 x 4096, full all the first square (2048x2048) fully transparent.
Is there any way to fix it? I could send you the pngs if you need to be sure I'm not doing something wrong.
Regards.