Roche says the machines that these tests run "automate the preparation and analysis of samples for quantitative and qualitative nucleic acid testing using real-time PCR technology. "
Please read the sources you linked to. The problem is the disease model and how the disease presents itself, how and where the samples are taken, etc. The PCR test is not what is the problem. Its the gold standard. We use it daily at our company and rely on it for our vaccine development. Don't believe me, ask any scientist.
Also, a minor point but I don't get the idea of replying to someone with someone else's opinion. That way I can't really respond to you can I? I'm supposed to find the original person and reply to them? .. Sorry.. just a pet peeve.