What are the problems that can be created by an unclean DWC system?

I am in week seven of my second round using my DWC system. This crop was just all kinds of problems and I am trying to pin point where the problems began. I have had all kinds of PH issues from the get go, the growth on many of them stunted, and even the roots had problems.

I running 2 DWC 20 bucket systems, black buckets all containing air stones and each running a 600 pump. The only changes I made from this crop to my last crop was this one I used grow stones. 36 of the buckets are stones and the last 4 are hydroton )Because I ran out of stones) I noticed that the four buckets that are in hydro got tall and big like normal, so I am wondering if the stones hurt my crop. Also, in between crops I flushed my buckets with hot water and wiped each bucket with a clean rag but I did not break them down and clean the PVC pipes and I didn't clean the tubing. Could this have been a problem?

You can accumulate alot of "crap" inside the tubing and such. If you dont want to break it all apart I would suggest Hygrozyme. After harvest pull your inner liners and deal with whatever medium you used (tron, rocks, etc). For the linners and buckets (I had a habit of tearing mine apart) I had the hot water, Dawn dish soap, a rag and the bathtub. For the system itself (if not broken down) do a good rinse down of the res then fill it enough to "flood" your buckets. After the amount of water needed to flood is in the res add amount of Hygrozyme from label of bottle. Flood the system and let it stay flooded for about an hour or so. Drain buckets and res and flush system with hot water. Hygrozyme is like an Organic roto rooter :D It will no doubt help eat the slime off of the inside of tubing.
If the only diff between grows was tron and rocks I think you have your answer already.