As I already told you at the other forum (alias Lucas), you most probably deal with a fungal infection here. "Damping off" came to my mind, but I'd put it a bit differently here, although the same or other fungi may be involved here.
First step to do, is work sterile when making your cuttings from mother plants and secondly, keep the growing environment cleaner as well. I am not a fan of sterility and lab atmosphere with hydroponics, but with cuttings you need to keep things as clean as possible. That is were the actual problem started most probably. Your wind shields are not the actual issue and all other things aren't the cause either.
Using a fungicide now, may help or not - it's questionable with the more affected stems anyways. I'd isolate the non-infected plants promptly, treat them as a preventive measure with an anti fungicide and would think of sacrificing the worst asap.
PS: what is the medium you use in your "aero-cloner"? I'd also consider a different media that doesn't hold that much moisture, as some synthetic plugs. Early inoculation with beneficial fungus as trichoderma would also be a good idea well that's what I use.
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