I haven't had good results with using a different seedling soil, so I went back to my usual Pro-Mix. Stick with what works for next year. Also, the seeds may be genetic duds to begin with. That happens. Unless it's ALL your seeds, then I'd say it's the soil if that's all that's different. How's your lighting? Need new bulbs maybe?

I've rarely had the issue of a first true set of leaves on a seedling being uneven in size, but I agree with Susan that it's genetic duds or old seed. Since you're experienced and haven't ever had this problem, I'd definitely think the problem is being caused by the one thing that's different: your starting mix.

Have you given them dilute fertilizer? suspect they need it. Then I'd probably transplant them ASAP and use Pro-Mix. ETA: oops... see you already potted them up. What did you use? did you fertilize them?

Seeds are a mix of purchased last year and new this year, and it's a mix of tomatoes, peppers, and eggplant. Potted up to regular Miracle Gro potting soil as I have every year, gave them a fertilizer boost, but so far it's done nothing. The only ones growing well are Cherokee Purple tomatoes and Golden Marconi peppers, but even they are smaller than I expect them to be right now. It's kind of heartbreaking.

I even purchased extra of the seedling starter because I liked how it functioned, but I think it'll find its way to the compost bin and I'll go back to doing what I usually do next year. Just strange to see the bizarre uneven leaves, so I had to ask if it could be anything else before I just straight out blamed the soil. The ones growing well are putting out normal sized leaves after being potted up, so I guess it's all the proof I really need.

I've had it happen with certain strains. I always chalked it up to genetics or the seed not opening properly.

Edit read your last post and it's sorta common with peppers. Also find it to be more common when seeds cling on to the leaf after germination preventing the plant from fully opening, usually 1 leaf can break free while the other is still being hindered by the seed. I use a spray bottle and spray the seed which will allow the leafs to break free of it. Actually this year all my peppers had issues with the seeds clinging on like that despite using a spray bottle, a few plants got stunted and a few died after germination due to the fact that they wouldn't separate from the seed. Occasionally I'll lose the odd tomato for the same reasons too. That's why you plant more and cull the weaklings out.

The last bag of MG potting mix I bought basically killed everything I planted in it. I won't buy ever buy MG potting mix again. I figure it must have been tainted w/ herbicides. It's a Scott's product afterall... the same people who don't mind poisoning the bird seed they sell!