It could be due to something called Candida "die-off" - if you have Candida that is. Here's a link which explains it better than I can.

http://www.holistichelp.net/candida-die-off.html

I use the probiotics in supplement form occasionally when I feel there may be a problem (eg diarrhoea) or if I think I might not have got enough in my diet with yogurt etc. Maybe taking a high dose probiotic could cause the die-off reaction - try starting with maybe one capsule every few days for a couple of weeks and build up slowly. Also watch refined sugar intake - this is food for candida.