Are your temps abit chilly?
Is the stem thinner than normal and woody? And its a bit purple right
I dont know how the stem would rot, i mean roots sure, but the section your talking about gets plenty of air. I would guess p def..
Wait a sec
Are you that dude i talked too earlier? If so then yea.. over feeding is causing most of your problems. Too much n will halt uptake of calcium. Calcium in High concentrations binds to phosphorus making calcium phosphate which is pretty insoluble
It also looked like metals were being locked out