My be it is fungi infection. The reused containers has to be washed with one part household detergent and 9 parts water and leave it covered under the solution for at least 30 minutes. You don't sanitize your backyard because you till it. Tilling kills most of the insect eggs and prevent it from hatching. As for sanitation of your garden soil mother nature takes care of that for you. Who can argue with mother nature.
Your leave problems could be too much or too little water, same with fertilizer and could be fungus. No one knows the panacea solution you need to experiment.

Possible root damage during transplant.
Possible root damage from drying out? and/or too wet? (Any drainage holes in the containers?)
Possible fertilizer problem -- to much? or too little?

These photos look like trace elements deficiency symptoms. Perhaps the soil lack certain trace element?

Have those been getting moved in and out, or are they very close to some warm lights? It looks like they are dessicated in spots, so maybe wind burn, sunburn or burn from touching warm lights? Also, generally don't use clear cups. I think there is a specific reason for it, but it is escaping me now.

My basil looked like that once I thought it was fertilizer burn.

No clear cups - because of negative phototropism. Leaves grow toward light, roots shy away from light.

My question about the plants is how long before they can be planted in the garden? The odds of a fungus infection are very slim unless they have been outside most of the time. If they have been inside then the odds greatly favor nothing more than environmental stress symptoms as already mentioned by others. It is an artificial environment after all. Contributing factors could be nothing more than transplanting stress, soil nutrient levels (the leaf tip burn), watering, ambient air temps, amount of light, and some scorch.

Assuming they will soon be planted where they belong they should recover.

JMO

Dave

Looks like sunburn to me.

* The soil is Happy Frog, no fertilizer added.
* I keep them within 1-2" of a T5 light, 14 hours a day.
* They have been in my living room the whole time, no wind.
* Water twice a week.
* Cups have drainage holes. No yellowing leaves, no algae.
* Humidity is around 30-40%, temperature 65.

Anything amiss?

Hopefully they will survive until I transplant. But I have doubts about a few.

Since you are using T5s you can back them off some. The 1-2" recommendation is for the older T12 bulbs. T5s put out much more light and heat. Try 4".

And with T5s I find 12 on and 12 off to be plenty. The 16-18 on and 6-8 off was also for older T12 bulbs.

Dave

Thanks digdirt, I believe you are correct. I backed off and they appear to be doing better. I actually had it at 15 hours. 12 hours at 3-4" is working better.

Yeah it is a point we often forget to mention - the big differences between the new T5s and the older type bulbs. Even T8s can be spaced a bit higher than T12s. And of course the number of bulbs in use can make a difference too.

Dave