JJWalker - I got this from atkins.com, hopefully it will be helpful for you :
I've had several episodes of diarrhea since starting Atkins. How can I avoid it?
Diarrhea is uncommon in people doing Atkins. In fact, people on Induction are more likely to initially experience constipation. However, some people can't tolerate dairy products?and consumption of cheese and cream may cause diarrhea. If this is the case, try eliminating all milk products and see if it gets better. Unsweetened psyllium husks can be added, which act as a sponge, soaking up water and helping form a normal stool. If you don?t respond to that treatment, then look at the amount of fat you are eating. If you have been on an extremely low-fat diet prior to starting Atkins, it may take your body a while to adjust.
If dietary fat is not the cause, diarrhea could also result from taking the recommended supplements. Try stopping them for a week, then if the diarrhea goes away, reintroduce them one at a time. So long as you have diarrhea, it is especially important to drink a minimum of eight glasses of water a day to avoid dehydration.