Okay, I worked out how to fix. If I'm understanding what I ready, the engine pretty much ignores your actual palette and uses what it has stored for the battlescape. So it's safe to open the image in photoshop, under the image>mode>color table (assuming the image is already indexed) and replace the transparent color with something like R:0 G:255 B:0 that isn't used in the tables. The image will now render correctly. Sweet.