aeroponics cloner (root problems)

From what I understand this is general used as an aeroponics cloner. I have a 350 gph pump with some pvc attached with 12 mister heads. I run this 24/7 and put ply clones in 3 inch net pots with a little hydroton to hold them up and the roots grow out, I use this set up for the entirety of my veg cycle, and so far they seem to do amazing. The only problem I see is on a few, about 3 inches above the water ( they all hit the water at about 2 weeks) the roots twirl around like rope, fairly tightly, before spreading back out again. At this point the roots are no longer white but brown, and in one case almost black. I am not sure if this is root rot, or the roots choking themselves out. Even with this inch or two of bad looking roots right in the middle (below being white and healthy) the plants don't seem to be suffering at all, they are lush and green.

I was wondering if I put the pump on a timer, 15mins on/15 off (smallest denomination my timer goes) would it hurt them, the roots are 80% hanging in air with no medium, so no sure if this will dry them out.

ps if pictures are needed I can get some posted.

Fifteen minutes off is waaaaayyyy too fucking long for the roots to hang dry like that. I've settled on thirty minute cycles in my aero cloner(TurboKlone T-24). 25 minutes on/5 minutes off, 24/7.

I tried 15 on and 15 off, and it seems to work, my plants were in no way wilting, but they did seem, I donno, a bit dryer, after a day of that. I would prefer 2 minutes on and 1 off, but unfortunate my timer is 15 minutes only. Right now I have it on for 45 and off for 15, its been like that for about 12 hours and I will give an update on that later.

I run my misters at 15sec on 15min off and have amazing growth speed, theres something else going on. Make sure light is not penetrating into your res. What is your water temp?

My water temp is between 55-70 it varies.

Also it only seems to happen on two of the 8 plants roots. The way my machine runs is a pump with a vertical piece of pvc, then a t joint, with a horizontal piece of pvc that has the misters. i noticed the two that had the discolored area, specifically the 2 inches or so of discolored root, were sitting directly against the pvc when the lid was closed, the area matched up perfectly, I have since moved it slightly to prevent this, its only been 2 days so not sure if its working yet, but the roots are looking slightly better.