I am a proponent for medicinal marijuana use - but in small managable doses. You haven't indicated how extreme your usage is. I am guessing it is in more than the small amounts I refer to.

There are studies out there that indicate heavier usage can be linked to anxiety - especially if you are using someing with a high THC content. One of the common symptoms to anxiety is gastrointestinal trouble.

Does any of this sound plausible to you?