Minor issue regarding Update#2...

Update 2: The PNG standard states that pallettes be 256 8-bit colours only, but apparently that is not always the case either.

That statement is slightly missleading. If you keep reading, you'll see that if your PNG includes a color pallette, then that pallette can contain at most 256 colors -- but you don't have to use a color pallette at all. PNG supports 5 distinct color types, including "truecolor and truecolor with alpha" in which case...

...the PLTE chunk is optional. If present, it provides a suggested set of from 1 to 256 colors to which the truecolor image can be quantized if the viewer cannot display truecolor directly.

BEGIN PURE SPECULATION...

Perhaps some tools (like GD, and the linux file command i was using) are incorrectly detecting the presence of a 256 color pallete as an indication of the PNG being "8-bit", when in fact it is a 24-bit (or greater) "true color" PNG.

(Of course -- since GD is clearly documented to only support 8-bit images, it might not even be trying to deal with the true color PNGs properly)