I highly doubt the stomach issues are from HCGenerate. I have recommended the product to hundreds of clients and never once has anyone complained about stomach pain or GI issues.
I suspect your issue is from the protein powder. Food allergies/sensitivities are a very interesting topic. You can go years eating a food daily with no problems and then all of a sudden, a food intolerance can occur.
It's kind of like how someone will eat a peanut butter and jelly sandwich for lunch everyday for 10 years and then suddenly be rushed to a hospital one day for a peanut allergy.
Most adult humans are sensitive to lactose. The milk sugar naturally occurring in dairy products. You need to be supplementing with a pure whey isolate, not a whey concentrate or concentrate/isolate blend. Stop taking the protein powder for a few days and I suspect all your GI problems will go away immediately.