KBS has never had any effect on my paints. But I only use water base acrylics. I have had other clears ruin my paint though. Like concrete sealers, etc.
EDIT... I looked up the paint you are using and found that they offer 2 different clear coats.. I'm not sure this would lock the color down. "9495 Aztek® Clear Matte or 9496 Aztek® Clear Gloss"
I have had trouble with some Rustolium paints... And this paint you use is made by Rustolium… There must be something different in their paint.