As a fellow reptilian modder I've been trying to puzzle out why their lips are always green for you and after you posted the raws I had a thought that yer invalid
[SET_BP_GROUP:BY_CATEGORY:MOUTH]
[BP_APPEARANCE_MODIFIER:WIDENESS:50:70:90:100:110:130:200]
might be causing the green, causing that bodypart to revert to default color. But when I checked it seems the default color for scales is grey... so much for that line or reasoning.
Anyway fixing that wideness thing might fix it anyway. Might be doing some weird stuff to the bodypart when it can't understand the raw completely. So after you do that might be worth checking on it again.
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As for the scales always being violet I think I know what's happening. The color modifiers are supposed to all be in one tag I belive, like so...
[SET_TL_GROUP:BY_CATEGORY:ALL:SCALE]
[TL_COLOR_MODIFIER:RED:1:CRIMSON:1:SCARLET:1:MAROON:1]
Each number is the chance relative to the other numbers to happen, which you seem to already understand. Just keep adding more colors to the tag til you have all the colors you want. With them all being separate tags they all overwrite eachother, until the last one declared, violet, is the only one that matters.
EDIT: Actually in the raws Sutremaine posted looks like he spotted that last bit as well. Ninja'd by an hour...blast.