The additional liquid is altering your fondant. If you add the color with the liquid, it will help. If you only need a small amount of a certain color, just reduce the batch to half or 1/4 of the full recipe.
then, you can easily knead in enough ps to have a better result.
What I do when I need to make dark colors (or a large batch of any single color) is to add the color to the melted MM's. I don't add anything other than a little scoop of crisco to my MM's, so depending on how much I need, I will put a few MM's into a bowl, melt, then add a bunch of color. Black is SOOOOOOO much easier to do this way. Once it is all mixed in I start adding the powdered sugar and kneeding it until it gets to the right consistenc. Most of the time I don't have to add any more color, but you should remember that you are adding white sugar to the color so it will end up lightening up a little bit.
Hope this helps!
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