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.

# EDIT

You can't develop an intolerance to isolate like you could develop lactose intolerance. I suppose you COULD develop some kind of dairy allergy, like a casein allergy, but that's not remotely the same thing as a lactose intolerance. If you develop some kind of allergy to whey or milk, than it'll present differently. You'll have an upset stomach, your lips will itch, you'll get hives, etc. Like any other allergy, symptoms will vary from person to person depending on the severity of the allergy. 

I suppose you could also be suffering some sort of allergic reaction to some other ingredients in the protein you're buying. For example, maybe you're allergic to peanuts and the new protein powder you're buying contains some peanuts. It could be anything. But in my eyes, its MOST LIKELY lactose intolerance.