A couple of things come to mind for me, first off what kind of bullet are you using? I have an encore and used to shoot Hornady XTP's. They always shot good and I killed a lot of deer with them but I would never get a blood trail. I shot a deer in six inches of snow one morning from about 30 yards. Good shot and we trailed her for over 100 yards before we found a drop of blood. She jumped a small creek and when she landed it looked like a bucket of blood had been spilled. I think she was filling up with blood. Last year I hit a doe and her front legs split and she fell on her chest for a second, got up hobbled into the woods and we never found her. I did some research on this site and other black powder sites and found some of the bullets similar to the XTP's are like a pistol bullet. They don't preform real well at the speed they are shot from a muzzle loader and can just explode on impact with bone and not do the damage that they should. Mid season I switched to a Barnes bullet and killed two deer with good blood trails.
The other thing I was thinking is that with a modern muzzle loader I sight mine in further then 50 yards. I have mine shooting about an inch high and 100 yards and have killed deer well over 150 yards and feel more then confident shooting at that distance. If I were keeping mine for 100 yards in or so I would just stick with a shotgun.
I know what you are saying about the smoke. In heavier cover I have shot deer and had know idea what way they went.