Many of the problems people might be experiencing with cloning might have to do with Pythium, the fungus that is responsible for root rot. Many systems contain some Pythium which can make cloning difficult.
First, Pythium is systemic and is often fund in the plant stem. The good news is that it can be defeated.
Pythium breeds well above 70 deg, in low O2 water. Plus, it probably prefers higher PH. It is an opportunistic pathogen which means it attacks vulnerable (weak) roots. The reason the aero-cloners are working is because the Pythium can not thrive in such an O2 rich environment. If stems are rotting, you may have a Pythium issue.
To overcome this, do not heat your clone solution, keep your PH low 5.7 or so and keep things well aerated. Of course clone machines do a great job of this. It might also help to soak cuttings in a light bleach solution (5 drops / gall or so) but this is experimental for me. Other than that, always scrape one side of your stem so the rootless plant can uptake water and keep in high humidity.
I have rooted the same strain many times with 99% success. When I discovered the presence of Pythium, this dropped to around 5%. I was lucky to save my prized strain and am looking foreword to a new batch of strong clones in my new DIY fogger powered clone machine.
Good luck.