Consider even a normal '06 barrel is considerably stiffer and stronger than most muzzleloading barrels, not considering length, which is also a detriment in this regard, to the ML. I can see barrel harmonics effecting the muzzleloading ball for sure. I've also seen it on target as when zeroed with a 55gr. 2F load in the 7/8" X 42" .40 barrel, prints 1" to the left and 1 1/2" low at 50 yards with 65gr. 3F. On the other hand, a 75gr. 2F charge, developing the same velocity as the 3F load, prints an additional 1/2" lower than the 3F load, but 2" to the right of it. Different harmonics of the 2F charge can only be the answer to the windage changes - in my opinion, of course.
The .375's are unto themselves for some reason. Every one I've had, puts 235gr. through 300gr. into the same basic group at 100 meters and case size doesn't seem to matter - full length magnum, standard length magnum, short magnum and standard '06 case Improved all show this characteristic. A 2" to 2 1/4" circle usually covers groups of 5 different bullet weigths inbetween the weights listed - that's 25 shots., with 5 from each. No other modern gun I've used, will do this and all muzzleloaders I've used also show differences with different charges, rarely in line vertically, but sometimes, do. The .69 shoots inline and fairly close to the same elevation at 50 yards - maybe 1 1/8" difference between 3 drams and 6 drams. Perhaps the .69 is the 'first' .375 magnum, however it certainly hits harder than the modern one.