Hey Cookie, what exactly are you taking?
I just started taking Green Vibrance, which has many probiotics in it. I was told that because of the high level of probiotics, that they will clean out your system and produce flu-like symptoms the first few days. I also find that taking them 30-45 minutes AFTER eating is the best time to take them, unless your supplements say otherwise.
Typically, they are cleaning out the bad bacteria, so you will experience some odd symptoms before you start feeling better.