Yeah I've got this problem too. Went through a bunch of tests with Kemper support as well. Support came to the conclusion that it was the pedals being overly sensitive to the send level of the profiler or something. Suggested to turn down the level in the cabinet module by -6db to -10db. Slight workaround there.
Try decreasing cabinet level till the problem goes away first. Pretty much the only parameter that helped with me.
I tried a few things that got some results:
{Main Output}: Off. {Direct Output}: Stack. {Aux In - Main}: 10.0. = No pedal distortion & clear sound!
-Also-
{Main Output}: Delay/Reverb wet. {Direct Output}: Stack. {Aux In - Main}: 10.0. = Same results, great sound!
Tested with four external guitar pedals connected to the send and return inputs.
On a side note: my countries Kemper distributer (innovative music Australia) wants me to send my Kemper in for inspection. They feel that's something is up with the way it handles pedals. Going to do it when I have time.