Maybe it is the soil.
I picked up a quarter bag of fox farms ocean forest they had laying around when the shop was out of promix. Since then, I've used it for my clones and for one seed. The one from seed (afghani kush) looks pretty horrid, and has for most of its life.
It was transferred to a pot of promix HP two days ago and seems to be improving.
I'll start the next seed in a cup of promix and see what happens, but for now I am thinking that my seedling didn't like the fox farms soil. The pictures are of the seedling (unhealthy) and of a clone (healthy), both spent time in a dixie cup with ocean forest, but the clone was only in it for a week after the cloner while the seedling has been in it for a month. I'll keep using the ocean forest for my clones until it is gone, but I won't be filling a full pot with it or switching mediums any time soon.