Purple, thinned stems stunting seedlings

[ScottinAtlanta]

Folks, I had great luck with 90% of my 400 seedlings, but about 10% were stunted. These seedlings were all in the potted up cups for 8 weeks, and subjected to cold treatment down to around 40-45 degrees. I notice that the stems of the stunted seedlings at ground level were darkened - purplish - and thinned. The leaves are green, so it does not seem to be damping off, but the root ball is very small.

Any idea what is causing this stem problem?