How crackle medium works is that the top layer dries out before the bottom layer. As the bottom layer next dries out, it then "pulls apart" the top layer, causing the crackle.
As you add paint, you're adding, a different medium so the crackle medium loses its effectiveness, resulting in the paint not crackling.
In fact, with craft paint, you need to put a thick layer of medium, otherwise, it won't crackle. It's like those dried mud flats. If there's not a thick enough, the mud won't have the crack effect.
Some tips on using hobby crackle paint (
GW's Agrellan Earth on bases) :
https://www.reddit.com/r/minipainting/comments/1sgpth/problems_basing_with_agrellan_earth/