I have multiple copies of each. For some reason the '61's are more accurate. There's no mechanical reason I can think of, maybe I just got lucky. Mason Stillwell and I both recently obtained EMF Hartford 61 Navies, and are really pleased with them . Great out of the box finish and fit, sub 2" groups at 15 yards with ball. Do a Google search for EMF's website, you can order direct from them, the 61's were on sale this summer for around $175.
I use about 20 grains of 3f black powder and a round ball (.375) for all my 36's. makes a good ding on the plate and still pretty accurate for CAStype shooting. You might want to back down to 15 grains, and then Cream O wheat filler , till the ball sits just below the chamber mouth, for best accuracy, target shooting.
Elmer Keith's book, Sixguns, says that Civil War veterans told him that .36 round ball and as much powder as you can get in the chamber and still seat the ball, was an excellent man-stopper.
Defineitly use Tresso or Thunder Ridge nipples. Smaller flash hole doesn't blow the caps back, plus they are a uniform size (dimension). Also, on Colt pattern pistols, polish the hammer face and de-burr the safety slot in the hammer face. A rough surface can grab the fired cap, and pull it off, where it falls into the action.
Only other clue is use lots of lube. Slather up the cylinder pin, smear some on the cylinder face, smear a thin coat on the face and sides of the hammer, and grease over the balls. I've never had a Colt C&B foul out or seize up and I shoot them in about eight matches a season, 100 rounds per match.