Try consuming more water with these shakes because sometimes your body will pull water from the body into the intestines and it will cause diarrhea. Also, if your protein is not very soluble/easily digestible, then it will be used to feed the bacteria in your intestinal track, therefore a higher chance for the runs.
If you are taking in a lot of protein at one time, like I do after an intense workout, then try to break it up into two servings. For example, I'll have my carb drink after my workout when I get into my car at the gym. Then when I get home, i'll have around 70 grams of whey protein in water. I will then drink an additional 8-12 oz of water and get into the shower. After the shower and approximately a half hour later, I will have the second part of my post-workout protein shake (an additional 60-70 grams of whey). As time goes on and my GI gets used to the higher loads of protein, I can eventually just have all my protein in one serving before my shower.
Another thing that you may be able to do is read the post that macrophage69alpha has on the anabolic board encouraging the use of GINGER ROOT. I think it is titled "How to eat more protein".
MR. BMJ