I'm back with an update after a 3-week break. As you will see in the photo below, my 3-leaf plant is now merely a 3-stalk plant with the normal pairs of leaves on every stalk and branch. It seems as though the 3-leaf trait was only carried by the main stem. Once I piched it back, the main stem ceased all vertical growth, but 3 branches grew where it was pinched instead of the normal 2. Those 3 branches have grown into 3 very healthy stalks, but unfortunately do not share the same 3-leaf trait. Oh well. Disappointed but not discouraged, I decided to try again. I had no idea what the chances were of getting a 3-leaf again, but I figured it was worth a shot. I quickly ordered another packet of the same seeds from the same supplier and germinated them. I'm only 2 days into having some sprouts, but it looks like I may have another 2 or 3 3-leafs coming up! If this is true, it obviously has something to do with this particular strand or batch, because I also germinated a 2nd round of 4 other basil cultivars and not a single one of them has produced a 3-leaf yet...only these Red Rubins. Now, moving forward. If some of these new sprouts do truly turn out to be 3-leafs, I would love to be able to keep this trait going. I'm definitely not going to pinch the main stem so soon (if at all). What I'm curious about is if there is some way to induce branch growth without pinching and sacrificing the main stem. I'm not implying that the branches would have anymore chances of being 3-leaf branches, but at least I'd still have a 3-leaf main stem and a plant with some branches on it. Thoughts? Photos of 3-stalk below. Here is a link that might be useful:

Grow it permiculture style. First off, basil does like full sun once it is established. Those single leaves have no self shading. The key is to plant them closer together and each time you clip the plant you pick off the leaves and put the stem right back in the ground next to the mother until you have a thick clump. Dead head-pull off flowers. If you live in a cold area, let the basil go to seed in the fall and stop harvesting the leaves. Plant all those seeds in the same place and mulch over for winter. In the spring a bunch of basil will grow. Let some of it go to seed and dead head the rest. After that you'll have a little basil forest.

I disagree. Flowering basil does not necessarily signal DONE. When some veggies go to seed , is called BOLTING. Like radishes. That signals DONE. But not basil, oregano, thyme, sage, basil, etc. Some basil varieties (Thai, cinnamon) constantly flower. if you let the flower stem to do its thing, plant will spend a lot of energy on it instead of new growth. that why best harvesting practice is pinching from tom, rather than picking lower leaves.

@Peter - No, I was using a bag of Miracle Gro Moisture control which I accidentally bought last year thinking it was a bag of MG garden soil. I have never used a bagged potting mix before, I usually mix my own and have for over 40 years. Still, everything else that was started in it over the past year has been fine. I even have a Jasminum sambac that I almost lost over the summer, repotted into the MG, which has since bloomed copiously and started putting out new leaves. I doubt its a great medium for long term use, but its been OK for seed starting other things, including my murraya koenigii, and in the short term for my jasmine. Years ago my preferred mix was 1;1 good peat and coarse vermiculite but I've not been able to lay hands on the coarse vermiculite for something like 15 years. Last time I special ordered - I ended up with a giant bag of medium grade, and then the nursery tried to convince me that was as coarse as it has EVER come. Sheesh! So I've been working with less than acceptable potting mixes. I have most often been using 1:1 or 2:1 peat-MG garden soil which, while not AT ALL optimal, at least let me start plants for putting out in the garden. It worked OK for container grown veggies too. It would have been horrible for houseplants - so I just haven't had any house plants for years until I picked up that Jasmine a bit over a year ago. Basically I haven't been happy with my choices for potting mix for years and this past year I've gotten REAL serious about finding a better solution. I'm still working on it. My son thinks I'm nuts, LOL! I have never had disease in my plants, other than cucumber beetles and squash vine borers spreading bacterial wilt and powdery mildew, I think it is, respectively - since they scared the few companies making rotenone into stopping manufacture of it for sale to backyard gardeners - you can still buy it by the gallon for fish kills, which has to be the WORST possible use for it - I have never found anything effective at protecting my squash so I've just stopped growing it at all. Row covers are too hard for me to deal with. Anyway I can recognize a lot of plant diseases but I've never actually HAD any in my own plants (other than the ones mentioned above). I had never seen anything like this on a plant, let alone a seedling still under lights, couldn't find anything that looked remotely like it - except maybe basil downy mildew, and scared myself into thinking that must be what it is since it looked so unfamiliar. Even the pathologist wasn't sure. The one lonely remaining Thai basil is fine - so were the other 2 he took for testing. But all my sweet basil was turning crunchy. I just can't think of anything other than accidental frying from being too close to the fluorescents that would have caused it. The Thai basil were all shorter than the sweet basil, and the taller the sweet basil was, the more obvious the leaf damage was. I would think some kind of disease - in fact I DID think it was some kind of disease - but the plant pathologist said definitely not - so it HAD to be some kind of mechanical damage. No fertilizing has been involved so it can't be chemical burn. I just can't think of anything else. Maybe sweet basil is just way more susceptible to leaf damage from even the fairly low levels of heat from a couple of fluorescents or something. I'd never seen anything like it - but I've also never been so fanatically obsessed with keeping the lights low (for the 20 curry leaf plants in the rest of the pak that came up at varying times so they are varying heights). Being that close to the lights hasn't fazed the m. koenigii at all - in fact they are growing great, if I can manage to stop underwatering them every once in awhile - but maybe the basil is just more tender. I'll try again with the basil, once I've got the curry leaf plants out of the flat and into individual pots on a different shelf. I'm just REALLY embarrassed that I scared myself into thinking my basil had a horrible disease and escalated it so far, only to find out there was nothing (pest or disease-wise) there. @gossamer - your state agricultural department will have plant pathologists on staff. Often they charge for this sort of thing - depends on the state, but funding is generally pretty minimal these days so they can't do as many things for free as they used to. In this case, they are watching the spread of basil downy mildew very closely. The plants were obviously damaged in some way, it didn't look like any typical basil diseases, and it was suspicious enough that they took the plants and did the testing. Check with your local extension agency first if you have questions about a plant disease and they can usually guide you to a state Ag department plant pathologist if it seems warranted.