I found out that my art software was changing my black areas from 0,0,0 to 5,5,5 for some reason.
Was it changing the bit-depth of the image? I would check this (I know latter versions of MSPaint do this when Saving, possibly to save space, but, for instance, say you only use 256 colours or less, it saves as a 256 colour bitmap regardless of the initial file.) This can be set with Save As.