As described in the wiki tutorials section
images for ground animations must have the same color palette as the image used to create the GBI for the map. This means you have to stick to 8-bit colors when making the images since else the color palette most likely changes. That greatly limits how you can manipulate the images. So to make the process easier I have written a program which copies the color palette from one 8-bit bitmap image to another. The convertion may create small color changes if the two color palettes are very different, but if you base your ground animation images on the GBI image (and I can't see why you shouldn't) the color distortion should be minimal.
Also, if you have lost the GBI image, the program can extract the color palette from the GBI itself but this may produce less satisfying results since GBI's only use 16 bits to store a color (and a 8-bits color palette uses 8 bits for each color component - 24 bits all in all).Changeset 0.9.1
- Severely boosted performance