Remove your dome as soon as your peppers sprout. When a plant goes from 99%- 20% humidity moisture is just sucked right out.Although domes are good at keeping moisture in for germination a sudden major drop in humidity can stress any plant .Once your plants start to break the soil remove it and just keep the soil moist until the rest come up. This is a common problem people have. Don't confuse a dome with a greenhouse they are 2 different animals. Try misting them a few times a day until they adapt to a much lower humidity level it might help.

pepperdave - thank you. That makes sense. You are spot-on, the humidity changed drastically.

Sounds like lack of hardening off to me.

Kevin

I have the lid cracked a bit to slowly let some air in. Over the next few days, I'll keep them moist and mist them once or twice. After a few days, I'll open the lid more and more until it's off.

Does that sound like a plan?

Sounds like a good plan.It is just like hardening off for humidity

I have never hardened off for humidity :(

Pepperdave - what is your hardening off process? How long does it take?

I think Dave is correct. I was shocked when I was reading that your plants were 6" tall and still under a humidity dome. I am surprised they did so well. Usually if the shear 99% humidity didn't hurt them directly, the mold, and other issues would have become big problems. But you said you transplanted them as well as taking them out of the dome. Part of the regression on the plants is likely the transplant shock that is normal when transplanting. Add in the shock of the humidity change and yes, you were giving them all kinds of "shock". I think your gradual hardening off from humidity is a good idea and I would gradually do it over 4-7 days. Each day, giving it more and more fresh air until they are free. Then it would be a good idea to introduce them to a fan gradually. This will simulate wind and also help to keep down the damping off fungus, fungus gnats and other problems that comes with growing indoors. It will also begin to harden them off (strengthen their stems) for when they go outside and get introduced to the real wind. Then, you will want to harden them off to both the sun and wind starting a couple weeks before you plant to get them outside permanently.

Good luck and post some pictures. We like pictures.
Bruce