Help - Not sure why pepper keep dying

Hi there,
 
First off, I want to say that I have been reading this forum for the last few weeks as my google search results have navigated me here for many of my questions.  I have decided to join this community, and I am very new to growing vegetables.
 
I'm having a major problem this year (my first year), and it is only with my pepper plants (habanero, wiri wiri, thai).  My non pepper plants (tomatoes) don't seem to be affected by this.
 
The first time around in March, I planted many peppers (started them indoors).  I had a very high germination success rate, and they all got their first true leaves and looked really healthy.  However, then I had a problem with aphids.  I think I perhaps diagnosed this problem a little too late, and I decided to purchase neem oil which is supposed to starve them over time.  Regardless, I got rid of the Aphids, and some of the peppers were looking really bad, but I still left them to see if they will be able to recover - they never did.  Some later planted peppers came up in around April, and these ones did not have the aphid problem, however, even before the true leaves would start coming up, the plant would start drying out, the leaves would scrunch up, and it would die.  After doing much reading, I determined that I was probably over watering the peppers, and that this was resulting in root rot.
 
The second time around (early May - 2 weeks ago) I started some more peppers with at least some experience this time around.  I now knew not to overwater.  I also went to a local nursery and picked up two pepper plants as well.  I'm very confident I am not overwatering this time around, but I am having a similar problem.  I am starting to think that this is some kind of a virus affecting the plants, especially because the ones from March gew so healthy for up to a month, and it was from then on forward that my plants would quickly become affected by this problem.
 
I am going to attach two pictures, one of some new growth (habanero) as well as one that was purchased from the nursery.  They both have the same problem, and the nursery plant is getting scrunched leaves.  That nursery plant by the way is in the same soil / pot it was purchased in, and it looked absolutely beautiful before spending the last 3 or so weeks in my house.  Please - if you have any advice, help!
 
New growth:
http://imgur.com/8J4PQoW
 
 
Established growth:
http://imgur.com/OydEZ6r
 
 I would have your soil tested . It may be too rich in nutrients ? Could be a virus but I kinda doubt that . The one plant seems to have some burned tips which usually indicates too much NPK . That can cause plants to go on lockdown and eventually die . They really don't look that bad though . 
 
did you poke a couple holes in the bottom of the cups?
 
That nursery plant doesn't look too bad besides the curled edges / burnt end on that one leaf.
 
I would still say over watering. That is the only common denominator between both your seed starts and the purchased starts. Only water when they start to wilt, and for sure, poke holes in the bottom of the cups. I have also read much debate about clear vs. colored solo cups. Light affecting the roots? I dunno about that. Are your purchased starts in clear cups?

Another tip of the day: as someone on here used to say all the time... "How about a good dose of 'leave them the hael alone". :D
 
I was looking at the pictures and over watering is what came to my mind...
 
OP, first off, welcome!  These guys will treat you right.
 
Secondly, when did you last water before taking those pics?  That soil (what type is it?) looks WET.  Depending on the soil it may hold a lot of water and require a lot longer than other soil types which have perlite and other things for better drainage.
 
Maybe it's "damping off" ??

I've had severe problems like that in the past as well. High death rates (very!) among seedlings. 

They look fine at first, grow up to 2, 3 inches, then suddenly go limp and die. 

Super frustrating. 
 
You should not use soil - get seed starting mix (soiless mix). Garden soil is fine outside, but inside the microbes that harm plants can be real problems - especially those that cause damping off and root rot (propably your problem).  Make sure all your containers are clean (use a weak bleach soak if they are dirty).  Plant more seeds per area at first 10 or so per square inch, and only in about 1.5 inches (depth) of soiless mix. Then keep warm (80-90 degrees) till they germinate.  Keep lights very close.   You also want a high root/soil ratio! This will keep them using the water that is there, and keeps the soil oxygenated. Stagnation and harmful fungus growth is minimized. Transplant to small containers of soiless mix - again though not too large at this stage (six packs or 1.5 inch seed starters).  Make sure they have drainage holes, but you can keep in a container that holds water, just don't keep this filled with water, only 1/2 inch, then let dry out before watering again.  You want to roots to take up the space in their pots (though not till they strangle each other!). The plants don't need much fertilizer till they have more than one set of true leaves, and then very weak solutions (there are many options). Then you can transplant to large containers or outside after hardening off (slowly exposing to direct sunlight and wind).  I like transplanting small plants, as they seem to acclimate quickly and soon grow larger than my large transplants! 
 
My first thought was fertilizer burn. If you purchased soil with fertilizer pre-mixed in, that could be all it takes. (Sometimes the manufacturer gets a little happy with the fertilizer. Unhappy for plants though.) Also if you are fertilizing the new ones already, you can stop. Those only have their cotyledons, which have the purpose of feeding the plant until true leaves take over. No need to fertilize until they naturally fall off. And yes, those really should be in starter mix, which has no fertilizer in it. The more established growth really makes me think of early fertilizer burn, because of the scrunching leaves. Depending on the source, assuming you have fertilizer of some sort going in there, you may want to flush the pots thoroughly to remove as much fertilizer as possible, or even consider repotting.
 
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