Could they be rootbound? Sounds crazy but when you transplant in stages the roots fill the container then build a little on the side, you transplant and they6 move out again and build on the sides you transplant again same thing. When you start in one pot the roots have room to stretch and grow without piling up somewhere till they finally reach the container and pile up while there is lots of usable soil in the middle, it wasn't used at the time because it wasn't needed. See if you can ggently pop on out of the pot oa little or look through the holes on the bottom and see how your roots are doing.