Lyman factory nipples are the suspected culprit there. I have read a lot of posts of people with Lyman percussion rifles having caps give them ignition problems. Get yourself and your son, stainless steel hot shot nipples.

http://www.rmcsports.com/rmcsports_cfmfiles/find.cfm item # ML092

Another trick is to put the nipple in a drill, and with some emory paper, spin them and thin the nose down a little. What I am guessing is happening is the first hammer fall is setting the cap and the second is firing it off in some cases. This will really become more pronounced as the fowling gets worse.