One way to avoid this problem is doing your final transplant 1 or 2 weeks into 12/12 next time. This seems like a classic case of the lime buffers running out in the soil, which usually takes 6-8 weeks.

Also growing from seed, 3 gal is a little small IMO. Even if the plants were vegged only a short time, I'd use at least a 4 gal, maybe a 5 for the final transplant.