Well, I personally use an Action script for photoshop. It is indeed not transparent but there's an alpha channel. I tried studying the PNG files but unfortunately they are completely different.
An alpha channel is a channel where Black means Hidden, White means visible, and the variations of grayscale indicate transparency.
That info was incredibly useful, thank you! By googling some of that (alpha channels), it led me to a program called "Advanced Batch Image Converter" (via a Ubuntu ask thread) that did the trick (except a very small few it couldn't convert) perfectly
! It is strange that Paint.net can open the images as they should be, but not GIMP. Silly, even.