Hi wicked1,
I had a a similar issue that stress me for so many months and it was really hard to understand whats was the cause (for reference this one one of the post I’ve made Issues for a persistent perfect level : accel calibration + autotrim/save trim).
After that I was thinking the origin was the notch filter applied, because when I disable it the level problem somehow was less present.
But it took me so many headaches to find out that the problem was the FC was to busy! too much processing!
First I was using loop rate at 800 and 1000 plus I had a custom firmware with additional calculations for an indoor localization system. This was the cause, asap I disable my additional calculations the level issue disappear.
…For this reason when I add to the chain the notch filter too, the quad became even worse.
Probably it’s not yours situation, but the symptoms you have seems exactly what I was fighting for so many month 
.