Quick update of the system, and why are the green onion dying ?

This week's update is not as joyfull as the previous ones, the green onions are dying....

Only one is surviving, the other ones are very (very) soft at the base. Yesterday I pulled the dying ones out, and besides the stem being very soft, some had surprisingly long roots. I am not sure what is going on. I am wondering if the now high nitrates could be responsible for it, or the high nitrite ( when diluted 1/100 it gives me a color so where in the 0.25 - 1 ppm range). The pepper seedling look good though and I can see 1 new leave on each plant at this point. Also, there are 3 new seedlings next to the parsley, I guess seeds that did not germinate before, so it seem that the "softening of the stem" is touching only the onions. The basil that died before was transplanted from dirt, and I suspect it didn't make it because I did not clean enought the dirt off the roots (the roots were black and rather hard). 

I keep checking the water every day, and so far, ammonia is at 0, nitrite at least 25ppm, and nitrate at least 100 ppm. More on this next week. Next post will be about a documentary I saw last week end.