What I suggest is exagerating the image contrast, like make it brighter, so that the very lowest colour your image uses is r16,g16,b16 or something like that - then replace this colour with black. It's caused by the colour loss between 24-bit and 16-bit, making very dark but not black colours appear as transparent. I often replace pure black with something bright to check for defects, then when I'm happy and the darkest colour is r16,g16,b16 - I replace the bright transparency colour with pure black.
I suggest looking into .PNG's and opacity masks, like for 32-bit images, the extra 8 bits is for the opacity colour, the brighter the opacity colour, the stronger the transparency. It's quite tricky, because I don't have a propper .PNG suitable art package (like PhotoShop, PSP is no good). You would'nt believe how much better opacity masks make your transparent images look when pasted over backgrounds or better yet, used on rotated plain objects like trees or grass patches.
Patch 5 does have some new Alpha mask commands that do the same thing, but a lot easier (I'm having to use memblocks to encode the opacity mask onto the bitmaps - only works in 32-bit mode). Hopefully P5 will be publically released really soon.
Van-B
My cats breath smells of cat food.