My first guess is they are too wet. Second guess is they should not have been fertilized until roots were established and growing in the new mix. Al

One of the most common problems with seedlings(of any type)is too much water. Potting soil(potting 'mix' is better)can also contribute to too much moisture around the roots, being more dense than the mix. The leaves will look like they're dry, but you should check the medium to see if it's too wet. The same thing can happen if the container you pot them up to is too large...the medium will hold too much moisture around the roots. How 'dilute' was your fish emulsion? It should be more dilute than what you would use if your plants were outside. And one other thing that may have happened is simply root damage from the transplant(we try to be careful with the wee ones, but...).
These are the first things that came to mind after reading your post. A photo would help if that's possible.
Cut back on watering and fertilizing, keep a fan blowing gently on the plants and see if they start to recover. Here is a link to someone having similar problems in the pepper forum that has posted photos. Check them out to see if your plants are showing similar symptoms. HTH

Here is a link that might be useful: peppers dying off thread

Thank you both for your thoughts. Man, a look the wrong way and boom! things start dying :)

I usually let soil dry out and then water. Perhaps it was the fish emulsion (perhaps not dilute enough?) or root damage, although its been a few weeks since that. In any case, unless the soil is bone dry I'm going to lay off these guys for awhile and hope they simply recover, although it seems once they start going downhill its game over. Fingers crossed for the remaining...I spent so much time nursing them. Sigh.

Thanks again for your advice.
Jessica

I have Pepper and Egg plant. I did seed them in March and they too long time to sprout. Noe they are growing very slow. I can not take them to the outside Garden that little. If I wait for them the season will be over. I saw at the Nursery Store Pepper and Egg Plant 10 times as big as mine. How did thay do that? I bought two dozens and thay still in my Green House. They look giants beside my little ones.

My sweet peppers are small too. Perhaps they started them before you in a hot greenhouse...peppers like heat. Mine are in my basement, in Wisconsin. I want to start getting them outside on warmer days, now that they are FINALLY here (although today its only 40!)

Jessica