Reading through your explanation I pulled a parallel line with model helicopters, as we do a lot of tracking and balancing troubleshooting all the time.
Although you have a set of perfectly balanced blades (mass wise, static balancing), if one blade is a bit twisted or airfoil is slightly deformed (factory error) you will never get the two blades tracking right. Now, being an experimental helicopter which lacks certification criteria, is it maybe possible that the two blades are not aerodynamically the same?
Although, you are starting to get my brain going... the cyclic lift change due to tracking issues - how do these effect the lift vector?
My thought is the lift vector also becomes a cyclic variation, as you have two blade tip paths to which the lift vector is perpendicular, but than you would also get vibrations in lateral and longitudinal axis.