Hi Irish86.
I've never taken it before and had to look it up. It looks to be an antidepressant and I'm not aware of it being used to treat Crohn's/IBD (I know that in low doses some antidepressants can be used for pain management). Was your doctor prescribing it for depression or were they using it as a stool hardener (it says it can cause constipation and for some that sort of side effect can be beneficial)? Says it can take up to 2-3 weeks to really start working for depression but with most meds you notice side effects fairly quickly and nausea is listed as one of the side effects.
http://www.nlm.nih.gov/medlineplus/druginfo/meds/a682387.html
I have taken antidepressants while on 6MP (for depression) but not that particular one. I never had any issues with the antidepressants and 6MP but again I don't know if you're taking it for depression or to help with diarrhea. If its for diarrhea, have you tried something like Lomotil?