Your experience reminds me of the instructions for zapping. In zapping you have to zap at least 3 times because of the sequence of things you kill. I will probably get the order wrong, but it is something like...the first zap kills the bacteria, and the parasite in the bacteria is exposed. Then the second zap kills the parasite, and a virus infecting the parasite is exposed. Then the last zap kills the virus. So, basically if you stop at the first zap then you will be affected by the para, and if you stop at the second zap, you may be infected by the virus.
I know, kinda confusing. But basically it means you have to finish or you won't just suffer from die-off you can come down with an altogether different illness. It could also mean that you may have to cross treat in the process. Like add goldenseal/echinacea to the regimen a few days after starting because it is better with bacteria particularly of the mucus membranes. Different herbs have their niche. Some have more anti-fungal properties, others more anti-bacterial, and some general anti-microbials. Combination therapy is usually more successful. Since many people don't know what the herbs they use are better at, they often don't complement it with an herb that is better at the other thing, or even realize that that a parasite can have a virus(who knew?!), and that it may affect them during the cleanse. So, no need to avoid anti-fungals, just be ready with some other complement herbs and it may work out better.