Colorado: Brass nipples? Can't be. They must be Ampco. I have never heard of Pedersoli putting brass nipples on a gun, nor do I think anyone makes them for the very reason you mention. That said, I ordered a set of musket nipples for my Kodiaks from Blomquist Percussion, preferring musket caps for large charges. You'll never get a millisecond's hesitation, even with Pyrodex, when using musket caps.
As to cocking both hammers, the locks are entirely independent and only sear/tumbler fit and hardness issues would cause both hammers to drop at once. I never had this happen to me and I have had two Kodiaks in .58 and one in .72, in addition to 10, 12 and 20-gauge Pedersoli double shotguns. If it happens to you, you'll know you have one or both locks in need of tuning.