I know it's been a long while since I've posted here, but I was taking a peek at the forum (had a bit of time) and noticed this thread - which I have issues with as well.
What I've noticed is that it's the second dose of my anti-microbials that really does this to me, and a bit of probiotics helps correct it. Now, who knows if I have the same issues as you do, Walkingbyfaith, but maybe it will give you a hint at something?
Best of luck with this!
Herb only treatment for Lyme & Bart ended 12/11 - no active symptoms for 2 yrs -Herb only treatment for Babesia ended 12/12www.healingwell.com/community/default.aspx?f=30&m=2977364
Had Lyme, Bart, Babs, RMSF, Ehrlichia, Myco, Anaplasmosis, EBV
New set of infections 8/2014 - still treating.
Come visit me: dogwoodtraditionals.freeforums.net/