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yes flax can cause intestinal irritation. try broken down flaxseed meal or omega 3s as a supplement to get similar benefit without the irritation. Black stools are sometimes a sign of dried blood in the stool. this is less often from colon cancer but from stomach ulcers/bleeding from a polyp or problem with the stomach or small intestine so that the blood is digested and black in the bm. (colon being more commonly red blood). Try over the counter prilosec this should be fine with any blood pressure medication-if no change within 2 weeks then see your gastroenterologist for a scope which is the only way to be sure.
this will more likely require an egd (upper endoscopy) than a colonoscopy to illicit the source by your symptoms.