I've been practicing a lot with settings and cannot figure out why the 2 and 3 stars are not matching.

All manual camera settings, set default to 0.1.
Its a very basic dusk sequence, nothing is blown out.
5Dmkiii
ISO: 100
started shutter at 1/200 and dialed down to about 1/50.
F4

In the preview window when I activate the holy grail wizard the jumps on the RIGHT are lower, I'm not sure if this indicates the problem or not?
I believe this has happened the last time I used the deflicker workflow as well.

Do I have a setting wrong in the software possibly?

No, there is not setting that will affect that. Did you check the compensations in Lightroom?
Maybe you did too much editing on the keyframes in Lightroom - especially Clarity, Lights, Darks, White, Black might introduce different looks for keyframes with different brightness. Exif-Data of your camera might not be accurate as well.
Try just to do the first step in the holy grail workflow and export the video from Lightroom after doing the holy grail wizard (without further editing the 4* keyframes) and check if it gets better.