Without pics, it's hard to say for sure, but it sounds like blossom end rot (BER). Peppers get BER just like tomatoes. It'd normally affect some but not all pods on a plant. Calcium spray (aka Bonide Rot Stop) might help you, although it didn't work for me at all. Basically it boils down to just tossing the bad pods and hoping for the best. The damage to the plants' calcium transport ability probably occurred long ago, with the heavy rains in May/June. Keeping the watering/rainfall levels consistent and even throughout the season is the only real defense. I'm not under the impression that soil type/composition impacts BER at all, either way. I have plants in Promix BX that got too much rain and have been plagued by BER all season; I have plants in cheapo Home depot potting mix that were under an umbrella during the heavy rains and never had a BER problem.