It kinda sounds like you might just be developing a lactose intolerance. People don't just start out lactose intolerant. People develop it as they age. After all, all babies start out drinking milk. Same thing happened to me. Drank milk and protein all the time, and suddenly started getting an upset stomach. There is lactose in whey protein, even without milk. If you get whey protein isolate however, there's almost no lactose. Try a whey protein isolate powder without milk. If you don't get an upset stomach, you probably developed a lactose intolerance.
Just a note if you do decide to try a whey protein isolate. Many companies advertise as whey protein isolate, even though they're actually a blend of isolate and concentrate. Whey protein concentrate does contain lactose. So make sure you look at the ingredients list and make sure it only lists whey protein isolate.