Vagus nerve - hyperactive microglia theory sounds very good, a step up from the individual pathogen theories the way i see it, but should be very testable via microglia dampening drugs. Apparently it didnt work in Wishful, thats a bad start i guess.
Because either the immune system isn't working properly, The infection load is to high for the immune system to go after all of the infection successfully, or biochemicals needed to do the job aren't available. Or all of these.
Healthy people may have stronger immune systems. Many of us have more than one pathogen - I had seven and working two kill off the bacterial pneumonias and beating back the viruses helped. I have seen people who have been ill for years finally figure out that they have infections and treating the infections has helped them. I think doctors are too dismissive or conservative and patients are not persistent enough, which has led to an awful lot of suffering. Dr Proal lays got a good case for being very inquisitive in the area of infections, and treating them.