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seeds Seedling help

Hey guys, I could use some help.  I have some plants in the ground that are growing heroically and putting out pods quite well, and no issues there.  However, I do have some need of help with seedlings.  I have started several plants from seed and had great luck with germination, but then shortly after that my plants seem to stall out.  For instance, the first picture below is of bhut jolokia seedlings that I started in a wet paper towel and progressed to the pots to grow larger before putting them in the ground.  That was about the first week in October.  The seedlings popped up quickly and set a second set of leaves, and then nothing since.  I would like to know what I have done or not done that has caused this, as it is very frustrating! 
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The second picture is of a red savina and razzamatazz plant, both of which were started about mid-October.  They grew great in the small starter cups, and then when transferred to the bigger pot they also stalled out.  Again, they have turned a bit yellow, but appear to still be alive, just not doing anything.
 
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The last picture is of Butch T Scorpions.  Again, they were germinated in a wet paper towel and moved to the pot they currently reside in, starting about the 1st of November.  They popped up nicely, and stalled out. 
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If I am doing something obviously wrong, please let me know!  I would really like to get the scorps at the least growing and producing.
 
What temperature are they in? I have just germinated some scorpions only a few weeks ago and have them in a little window box under a light temp is 20-25c and they seem to be doing fine.
 
They are outside in indirect sun most of the day. Right now that means 25-32 degrees, with a few nights down to 20. The temps here in Queensland are pretty good, and I figured that outdoors was best. Not in direct sun mind you, as I don't want to bake the little plants!
 
Yes, germinated in damp paper towels in ziploc bags on top of the fridge. Once the seeps sprouted they were put in small pots outdoors and have been there ever since
 
A similar thing happened to me, where I germinated bhut jolokia, moruga and red savina seeds indoors.
 
About the time their first true leaves emerged I decided to transplant them into slightly largely cups and leave them outside in a shady spot.
 
They still however did receive some sunlight, minimal at best but it was unseasonably hot at that time here in Sydney.
 
Needless to say the same scenario occurred; the plants growth stopped in it's tracks and even after bringing them back inside no visible growth for 4 weeks.
 
I abandoned that plan, a lesson learnt I guess.
 
Since then I've done some experimenting and I found the best way to germinate these particular seeds and ensure growth is to sow the seeds in a cup to begin with (cup placed in a sealed storage container on top of the fridge) and as soon as it germinates put them by the window for some daylight.
 
When the sun goes down I put the cups under fluorescent light and turn them off in the middle of the night so the plants do have some darkness to ponder in.
 
The other alternative is to sow the seeds outside to begin with in a spot where it doesn't get too hot.
 
I used the cup method basically outside from the get go and the plants showed no stunting or irregular growth patterns.
 
 
If you were to remove the seedlings from the soil I highly suspect there is minimal root growth. This is what I experienced with mine and once the seedlings growth stunted it was very hard for them to 'snap out of it', in my case they never did.
 
Hope your seedlings can get going again mate, I know how frustrating it can be....
 
 My guess would say the soil is  not drying out fast enough. Too much water will cause a plant to go dormant and eventually die. Could also be too many nutrients. That will also cause them to go dormant.  
 
I do water these more than the well established plants that are in the ground, but that was because I was concerned with how small they were that the hot weather would kill them off.  I think I will try letting them dry out a bit, and see what that does.  Clearly they aren't doing much right now anyway!  Will a seedling let you know that it needs water far enough in advance that it won't die in the interim?  A few that I had seemed to dry up into nothing over the course of a day, but they ended up in the direct hot sun also.
 
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