I really can't help you because I've never had a problem with my gel colors being lumpy. I don't like to use gel colors for painting, though, because it sometimes doesn't dry very well. I prefer powdered colors mixed with vodka.
Angela from "The Painted Box" has a brilliant tutorial on this. I made several jars of color to use on fondant and such when I was in Alaska and her method worked brilliantly. I didn't pack them up with my moving goodies, sadly.
The gunk is just the thickener and she'll explain in the tute. I'll make some more when I can as it worked so well for me.
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