FIXED: Hi, I've discovered a fix for my issue.
The issue seems to be the software I was using to draw and export my assets. I use some freeware called GraphicsGale to create art, and the issue seems to stem from a bug in that software. Even though it seemed to be exporting correctly to my filesystem, something in the .png formatting must be off enough to cause it to get rejected by itch.io.
To remedy this, i opened my assets in Gimp, and then just re-exported them as .png's. This allows me to upload favicons and banners with their transparencies intact. I hope this may one day help someone experiencing a similar issue