This is the formula for figuring RB's BC's that I've seen:
B.C. = Ball Wt. in grains divided by (10640 x ball dia. x ball dia.)
Example: For a .535 ball weighing 230 grains, 230 divided by (10640 x .535 x .535) = a BC of .0755. Lyman's Black Powder Handbook gives a BC of .075 for a .535 in. ball, so the agreement is good. This formula courtesy of "Lee in Denver"
A .490" RB weighs 177 grns, which, according to the formula, has a BC of 0.069285.
Is this different than the formula you are using? Maybe this could account for some of the differing trajectories.