It depends on what type of protein you are increasing, but i know i became gassy and uncomfortable when i did that. Everyone is different though.
What is your dilemma?
Your body might just need more time to adjust? Increasing something and taking things away that your body has had for a good amount of time can make your stomach a bit off. You might just need to let your body adjust. Then again this might have nothing to do with your stomach. Hahaah. Sorry my stomach used to hate me so i base everything off that.
Then again i'm not sure what you are going through.
Sorry if that didn't help.
I will probably wake up tomorrow morning and read this and it will mak no sense. Hahaha. Sorry.