C'mon man, you must be shooting cheap production made flinters to have all those problems! Try shooting one I built sometime, by the time your optical nerve registers the pan flash, the ball is already out of the bore. Everytime I've been at ML shoots, I see the percussion guys spending more time poking at their nipple holes and snapping caps than shooting - the most reliable percussion gun is an underhammer, almost no problems with u/h's compared to sidelocks, especially the snail-breech sidelocks.
Yes, a flintlock must be set-up correctly and that should be done when it is built and never requires adjustment unless something breaks. Try shooting a quality hand-built flinter with a tuned lock & trigger, a single point cut rifled bore and good sights and you'll find your percussion guns becoming "safe queens" rather quickly.