I have the same problem as you.
Whenever I include a protein supplement in my diet (whey concentrate, isolate, MPRs, etc.. whichever it may be) I end up with severe flatulence and constipation.
My body doesn't like protein powders. Period.
Learn to listen to your body and eat according to how it responds best.
For me, that means eating some carbs and fats alongside my protein in EVERY meal (except my gatorade when I finish with the weights ofcourse).
I know it sucks to eat 4-5 egg omelettes instead of just chugging down an MRP. But hey, you gotta overcome.