Just fixed this in #jcstalk with Unknown Rabbit, thought I'd let people know so they dont boggle their minds about it

Anyways, here's a new lesson for the day when making tilesets:

When you're making the tileset for things that are hard coded into the palette (snow, pinball tools etc.), make 100% SURE that the colours you used are placed inside our tileset image! It would be even better if you made a mini drawing of your palette inside your tileset.

Fact of the day:
If there is any palette entry not used in your tileset (even if you put a different colour than black there), JCS will replace that entry with it's own colours.

And BELIEVE ME there's a lot of them, I was shocked when I saw it all.

Problem fixed, have fun making tilesets