Although I'm partial to flintlocks, I have to disagree w/ you on actual experiences of the reliability of flintlocks VS caplocks in the rain. Have hunted w/ both in the rain and the caplocks require far fewer requirements for reliable ignition than w/ a flintlock.
More precautions have to be made w/ flintlocks in rainy weather than w/ caplocks and perhaps the flinters realize this and take all the precautions....and the caplock users might not, judging from your stated observation.
A few years back hunted elk in Colorado w/ a caplock and it rained 8 0f the 9 day season...sometimes in only a drizzle but sometimes in a downpour. After 5 days I thought the load should be fired and a fresh load put in. The "old" rained on load fired w/o incident.
Analyzing the 2 ignition systems reveals that a tight fitting cap will not allow moisture to pass through and the properly lubed PRB won't either. So....what's left that would "deaden" a load in a cap;ock? Condensation would be a possibility, but if the caplock rifle isn't subjected to big differences in temps, condensation wouldn't happen. This also applies to flintlocks.
The main target of unreliable ignition of a flintlock in rain is the prime and an open TH. The prime and TH can be protected w/ a calf's knee and if after a shot, the pan is thoroughly cleaned and dried, the new prime under a calf's knee will provide reliable ignition in the rain. As far as the TH....my experience has been that I pay no heed to it....of course my TH liner has always been reliable, but some might require "picking".
All in all....more things can go wrong w/ a flintlock VS a caplock when raining, but the flintlock can be as reliable as a caplock....if all the precautions are taken.....Fred