Howdy Good Time Charlie,
I think what you're seeing is the difference in the weight of the projectile (plus higher velocity of the smokeless load).
The ROA sights are based on using a .457 round ball that weighs in at around 148 grains. When you use a heavier projectile, the bullet will impact higher on the target. When I shot cartridge in my ROAs with R&D conversions at 10 to 30 yards, I usually had to hold closer to 6 o'clock instead of my blackpowder hold at center of target. I was shooting 250 grain bullets reloaded to about the same velocity as my BP, around 725 FPS.
If the smokeless load is faster, like 800 or 850 FPS, it will also change the impact point.
There's a couple of us who shoot Vaqueroes, .45 LC at 85 to 1-200 yards. With cowboy smokeless ammo there's some drop at 100, but the Vaqueroes are sighted on modern ammo and heavier projectiles. The .45 LC shoots pretty well at 100 yards.
I have loaded ROA roundball in .45 LC cartridges and shot them in my Vaqueroes. They hit quite low compared to the 250 grain bullets the Vaqueroes were sighted on.
Hope this helps,
Watt