Well I always made my black number 2 on the pallete. Because JJ2 treats the 1st colour as transparent (I think). I don't know if this is accurate, but it worked for me, so you might want to try it.
Also, even if you change the black in spot 1 to another colour, it will still treat it as transparent. You need to put the black colour somewhere else in the pallete.
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With our extreme gelatinous apology,
We beg to inform your Imperial Majesty,
Unto whom be dominion and power and glory,
There still remains that strange precipitate
Which has the quality to resist
Our oldest and most trusted catalyst.
It is a substance we cannot cremate
By temperatures known to our Laboratory.
~ E.J. Pratt
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