Hello~It has been said that approximately every 5 years or bodies and allergies can change, so, you could very well be having a type of allergic reaction to the peppers. However, from what you have described, I would say it is more like a "sensitivity" both can be bothersome however.
As to any long term effects from having the bowel issues, I doubt if it will cause cancer, but, possibly, you could developed an inflamed intestine or tummy lining. I would stop eating the peppers for awhile and then add them very slowly back into your diet, one by one, see how you body handles them.
Also, add a good, pro-biotic to your diet, this will keep the friendly bacteria in your gut that the prolonged diarrhea is removing. This can also sometimes help with allergies and sensitivities.