I also have fevers with flare ups. I generally have sub normal temps, so when I start to hit 99 degrees, I'm not feeling very well at all. This will usually occur in the late afternoon on days I've been pushing myself and/or am just in flare. An all out flare will produce fevers 100- 103, along with headache, and body/muscle pain. The fever usually subsides over 3-4 days, but it takes longer for the fatigue to diminish. However - there is some question about this being from chronic epstein bar/chronic fatigue, or an autoimmune condition - something the rheumie is trying to figure out. I have not been under the impression that fibro causes fevers with flare, and it isn't uncommon to have dual conditions of fibro and an autoimmune problem. Be sure to tell your doctor/rheumie about the fevers. I also seem to have some liver involvement during the flares w/ fever - enzymes go up, along with CRP, etc., so perhaps some bloodwork would be clarifying as well. I chalked up everything to the fibro dx for years - before being referred to a rheumie. So my advice is to keep a journal of your symptoms and fevers - as well as your normal temp - so you can get a good feel for what is going on and talk to your doctor about it.
Prior to fibro my temp was always normal. Now my "new" normal is 99-99.3 when I go to my Dr's appointments. GamJill