Rancid...?
Some nuts and seeds are not cared for and turn rancid ~
Also, how well are you chewing the seeds? My roommate ate seeds without chewing throroughly once and had the same reactions - until he made a paste in his mouth when he consumed them.
ALLLLSO as you already suggested, perhaps it's a reaction to parasites? I had similiar experiences when I first ate raw pumpkin seeds - and even through the horrible pain I felt, I had an insatiable craving for them. Now I can eat them whenever I please. :)
Lastly, if your liver is clogged full of gallstones, your body has a more difficult time breaking down fat, and responds with diarrhea, vomiting, ect.
Have you tried The Wilderness Family brand...? I know they are very careful with their products. You may choose to look into their pumpkin seeds [and all other products! :)]
Lemme know how it goes, please!