i dont know why they try to root above soil jensen... lol, could be moisture near/on the lower stem as you suggested, not only that but that is its main root area so i would expect it to find the most viable place to root. constant moisture, constant oxygen and near darkness would cause roots. you can make a plant root halfway up a branch if you give it the right conditions and some people do this rather than take cuttings, they root the branch on the plant first. then cut it off and plant it straight away. no humidity domes, no cloning rooms/tents.
as for the your stalk john doe, i cant really tell from your pictures but you will know if it is stem rot. day by day it would have got seriously worse. the stem would start to become squishy and brown not like bark at all, have a feel... does it feel like its getting rougher and stronger or is it becoming more soft and pliable. if it was any kind of mold then again you would be able to tell as you would easily be able to wipe and smear it with your finger, mold growth also accelerates the more there is and i think by now it would be very 'hairy' (mold). Try and get a clearer picture of the area your on about and maybe we can identify it, but imo, i really think you would know by now if you had any kind of mold/rotting issues. this could also be a hyrdo thing which i have no experience except for early nft systems and maybe better suited for someone with hydro exp to explain.
and so the process will continue...
