Is that a remap, or did you use the palette trick? (make all sprites with one palette, edit the color palette on one frame, and declare that as the palette in the entity's .txt)
If it's a remap: either the icon or the remap isn't properly recognizing the pixel alignment of the colors. Make sure your icon uses the same color placement as your remapped sprite.
If it's the palette trick: I encounter that problem all the time. You have to make an icon sprite from the new palette; because the palette trick changes the colors on every sprite in the entity EXCEPT the icon.