Having some trouble retexturing sprites

So i've got the sprites edited and saved with a transparency layer added, but now i've got an issue. pretty well any amount of white(even in the grey tones) is transparent this isn't completely horrible but it affects all the greys, and any color mixed to a certain illumination. the program i use to edit the sprites is paint, followed by gimp to add transparency layers. please help me figure this out 90% of this was just so that i could combine multiple packs and edit colors on certain items