My suggestion until it is cleared what is causing it, my suggestion:
Clones become color-values from the Cloner Object, or (based on the set up) from the Effectors as well.
The “Color” that the Cloner Object provides is part of the cloned lights as well. To have two sources that can influence the light is not really my favorite thing to animate, if one source can do the trick.
Leave the intensity to 100% (not animated at all!) and animate with the Cloner Object>Transform>Color. This might help to get stable results, at least I get it here in this way.
All the best
Sassi