OK, I'll weigh in on this one... I have a similar problem with my Traditions Hawken .50 percussion rifle. First shot from a clean barrel is always low and left, about a foot or so. The load I'm using is PRB under 70gr FFg Triple7 and a CCI #11Mag cap - which produces 3-shot groups very consistantly under 1" at 50yards (not including that pesky first shot). After consulting with the fine folks on this board I tried a few of their suggestions. Here's what I've tried so far:
1) Clean the rifle without disassembly - have discovered that using hot water sprayed through an engine washing gun using compressed air works like a charm. Makes it easy to keep water out of places it shouldn't be (and isn't all that expensive, Walmart sells the engine cleaning gun for under $15). And when the rifle does have to come apart for cleaning, I make sure to goop the heck out of all the metal parts with lube to ensure that, even if water does come near them during cleaning it won't actually get to touch the steel.
2) After a normal cleaning which includes disassembly, swab the dickens out of the bore with a heavily-lubed patch. BTW, the only thing that goes in my bore is bore butter so there's no chance of petroleum contamination, even after a cleaning (unless the gremlins pour oil down the barrel at night when I'm not looking!). I don't even use oil-based lube on the outside of the gun, but rather use a lanolin-based lube called Fluid Film. This is great stuff for protecting metal, sticks like the proverbial you-know-what to a bedsheet!
3) Clean all lube out of the barrel using alcohol-dampened patches, then shoot the gun with a dry bore.
4) All of the variations above, with anything from only one or two caps fired before loading up to 10 caps fired before loading (using the fouling from the caps to kind of 'season' the bore)
The net result I've seen so far is that none of these techniques works very well for bringing that first wild shot back into the group. The best improvement seems to have come from not disassembling the gun, combined with swabbing the heck out of the bore with a heavily lubed patch, followed by snapping off about a half dozen caps. But that first shot was still a good 8" off the point of aim. And darned if the second shot doesn't punch the centre out of the target.
I guess these little conundrums are what keep us scratchin' our heads and pullin' our chins, and enjoying the muzzleloading sport!