Well, two days after I read this post I came down with the flu (as well as did my entire family over the past 7 days)! It has never taken me so long to get over the flu before - 4 days and counting. My fever just went away yesterday.
I have noticed a definite increase in pain, to answer your question about flu and flares. My muscles are much more sore to the touch and I have a feeling I will experience a gradual, rather than sudden improvement.
Hope you are feeling better. I am back at work today, finally.