I was diagnosed with fibro/cfs in 2001 by my MD. I have used natural herbs/cleanses and some kill bacteria. I always notice when I do these cleanses and stick to a low carb, sugar free, healthy diet, my fatigue levels, brain fog, body pain is cut in half or therabouts. Definitely pathogens are a factor in fibro/cfs if I go by my experience and the research I've done from many sources. I don't know if a single bacteria is the originating cuase, but I could see how taking a medication that kills pathogens woudl make a huge difference just because I've seen how taking herbs that kill pathogens has made such a big difference for me.
Hold onto hope and follow your instincts.