Flax can have a laxative effect, including causing mucousy bowel movements. The mucous can be from you, or it can be the mucilaginous flaxseed itself, which gets all gooey in the presence of moisture.
Just want to say quickly that I was doing the ground raw flax too and it was making me feel like I was being poisoned. Seriously. I could not sleep and had to drink gallons of water. This would go on until I pooped it out. Then suddenly I was fine. So much for it being healthy! I had read it was better to use it raw, I am much too scared to try it again, even cooked. So yes, I think you can have serious issues with it - probably from the cyano compounds.
I don't know about hemp seeds. I'm a bit nervous about that, although have had some stuff with small quantities of Living harvest hemp milk and done okay. Need to do a trial at some point.