Unless you really over-did it with fish fert, I'm somewhat stumped. Every once in a while I get a plant that just has weird genes.
As for the whole CalMag thing - I think lots of folks use calcium in particular trying to solve a problem that isn't directly related to lack of calcium. As an example, tomato plants only need about 14 mg/L (~ppm) Calcium, and they are a plant that needs more than most. Everyone and their brother says "give it Ca or Mg or CalMag" at the first sight of blossom end rot.
Ca and to a lessor degree Mg are not particularly mobile within plants. Tomatoes can't even absorb Ca ions through their fruit or blooms, so spraying it on doesn't really do anything. If everything is in balance and you're irrigating with water from a drilled or dug well, creek, river, lake or municipal water, there is more than likely enough Ca and Mg in the water for the plants. I'm growing a really finicky roma-style tomato this year and some of the fruits got blossom end rot. I just added more water, picked off the bad fruits and it went away over the course of a week (new fruits showed no signs of BER). Haven't had any BER-type symptoms with my peppers this year, they seem to really like this incredible heat.
Only other thing I can think of to ask is: What type of soil is it planted in? It's a relatively small pot so salt build up is a possibility. Given anough water, love and time, plants tend to be smarter than we are and correct themselves - since we're harvesting the peppers off of these plants, that's the last part of the plant it is going to allow to die since its peppers are the source of its reproductive cycle.
Good luck!