Hello Kathy,
Miky here, from what I  know about CS, what you are experiencing is not 
unusual.
The amount that you take may be to blame. I use it sparingly, I brush my 
teeth in the morning and then I swish a Jigger of CS 30 seconds in my mouth and 
let the absorption take it place in my mouth then I spit it out. This is what I 
tell all the first time user's that use this potent stuff. Depending on the 
degree and type of  infection that you might have..bacterial infection ..not 
unusual... Some times viral or a combination of the two.
 
Viruses will attack bacteria. 
The only thing that viruses are good for are population control.

When you use CS you must drink at least 8 glasses of water a day.(Or More) 
This will purge your system of dead micro-organisms, that Have been destroyed 
by 
the CS. This will prevent any HERX reaction. A Herx Reaction will make you 
Feel sluggish and you will feel tired. When you feel like this you must cut 
back 
on the amount that you use or stop using the CS for a while. Let your system 
catch up. Drink water... pure clean Water.
As for the stomach upset.... Eat yogurt, this will usually settle your 
stomach.
Also cut back on the amount of animal proteins that you consume. 
Meats are hard to digest, and Using the CS inconjuction..... well you get the 
picture.
I am not saying cut out all meats, just reduce the amount that you would 
normally consume.