I was able to resolve my issue in a weird way. I noticed that the performances that were having the issue all had "Ducking" set to +0.0 (which had an audible difference) instead of <0.0> (unity) and I was unable to change the setting to <0.0> even if I removed the effect and re-added it. I had to set up a new stereo loop in a new performance and then lock the FX block and switch to my original performance, which applied the locked setting and save the performance and repeat this for each of the affect performance blocks.
Not sure if this is a Rig Manager bug or a Kemper OS bug, I did not try to do it manually on the Kemper, but the takeaway is that +0.0 ducking performed very differently for me than true unity <0.0>.