I had the same doubts last month as my crop of sannam and Pusa Jwala (Indian hotties) have refused to redden due to cold freaky summer and late planting.
But yesterday, I ate them and found that they could jar me awake from deepest slumber. Man ...they are HOT HOT HOT.
The flavor is just wonderful.

But you might be correct about jalepenos. I bought local Michigan jalepenos and found them to be both minus heat and flavor.
May be this differs from variety to variety.

NJA

Same here. Most of my plants are still growing and producing pods, but compared to August, they are smaller, a bit less flavorful, and way, way, waaaay less hot, especially the Jalapenos. My Biker Billys, which were blazing hot during the summer, have virtually no heat now - they're like bells.

If your Biker Billys have no heat, then the cooler temps. must be the reason. I make up a mixture that I use for chilli and use it throughout the winter. Quess we will have bland chilli this year. Thanks

I'm actually pretty frustrated with the non-pungency of my recent colder-temp pods. It got really cold here in VA about 3 weeks ago - nighttime temps are down in the 40's. It's not just the Biker Billys that lost their heat. We made a habanero chili and ended up throwing a tablespoon of hot pepper powder into it because it had little heat. Habaneros! Without even enough heat to make a bowl of chili satisfying. Lesson learned for next year. Where is that global warming when you need it?

I am pretty sure of what I am growing next season. It is Pusa Jwala for me because even at temps so low and mild summenr, my green pods are packed with a wallop like a mule kick. I will also grow my daily intake of Naga Morich/Bhut jolokias.

I wonder if humidity may be a factor. Capsicum may be anti-fungal, Perhaps plants make more in wet humid conditions?

I have only had heat issues with the jalapenos I am growing this year. The only ones that had any heat were my Billy Bikers while Jalapeno M, Jalapeno Gigante, and one other variety had no heat at all. As far as my other plants they have kept on par with thier high heat levels.

I assumed that it wasn't so much heat as stress that affected pepper pungency. I noticed with my Anaheim chilis that during the blazing heat of mid summer they produced smaller, very hot fruits, while during spring and fall they produced larger, milder fruits.

I thought it was because they were under stress from being both hot and dry. If that's true, maybe a solution for this cooler weather would be to water them less? I haven't experienced it with peppers, but I have heard that holding off on water can make tomatoes and melons more flavorful. It might be worth a shot.

Of course, if it's cold AND rainy then there's not much you can do about it.

seasonal temps will change the heat of the pepper, what can be done? not much. watch the fungus factor, that takes most growers down fairly fast.
good luck! happy peppering

I just had the same experience of my jalapeno and Serrano peppers losing all their heat and I thought it might have been the heat wave we just had, so its not the air temperature. Nor is it humidity because where I grow its always dry. So maybe its day length? Still looking for an answer. but what a disappointment when there is still such a large crop on the plant. And now I have to keep the sweet ones separate from the hot.

Some of my chilies are very bland this year, and we've had a very hot summer. OTOH, I get very hot chilies in the winter, and so there must be other factors involved. I tend to believe that some plants just make hotter chilies, and some plants make milder ones. Hot weather has not made my chilies hotter, and cooler weather with short days had not made them milder. The age of the plant may be somewhat of a factor - I've noticed that plants over a year and a half old start making somewhat milder chilies. I generally try to replace plants when they are more than two years old.