Not sure if the cold wet weather is causing the dark spots or not but it probably isn't doing your peppers any good. Prolonged temps below 50 are tough on peppers and the wet weather probably isn't helping. Unless the temps are getting below 40, the weather probably wont permanently hurt them but will likely slow their growth for a while until conditions get better.

its just wierd that none of the other plants (chilis,jalapeno,bells, and habenero) are showing the same thing.