Cara,
I just read this on my son's nutritionist's website:

OBSERVATION: Laurie takes acidophilous , a “good” bacteria product, to improve gut function. The result is irritability and/or increased gas and loose stools.

WHY? War could be raging between “good” and “bad” bacteria in her intestines, causing symptoms associated with die-off. Healthy bacteria are replacing the potentially harmful bacteria or yeast. As the bad organisms die off, they release toxins and irritants which cause symptoms.

ADJUSTMENT: Lower the dosage of the current supplement or try a less potent product. A slower, gentler approach can achieve the same outcome with less distress. If symptoms persist, ask your health practitioner to suggest tests to understand the digestive environment better.

--Judy