no all this growth happened after the transplant!
I started it in a 2.5inch pot and transplanted it when it was rootbound to a .5 gallon before it pushed for its first leaves, the stem that I was talking about in the original post is the withered bit under the new stem
Then when I posted later that I was gonna dig it up, I repotted in a 5 gallon with the seed part totally exposed and gave it life support treatment for 2 weeks .. new stem shortly after. voila! The plant who lived!
thanks fruit nerd, you may have made all the difference : )