no big deal but weird lol

Nonfat yogurt makes me nauseated and sick to my stomach but nonfat Greek yogurt is fine. Neither has more sugar than the other. In fact, the nonfat yogurt has 20 less calories than the greek alternative.

Weird, huh? Lol :)

I have something similar.  Odd isn't it

It's probably because the whey is strained out of the greek yogurt.  Some people have issues with the whey in dairy products. 

....so does that mean 100% whey protein isolate (instructed by my NUT as the preferred choice) will cause more issues in these people than other protein powders?

Probably not, the way the isolate is processed is generally easier to digest than other protein powders. Some people will have issues, but that's true of everything, isn't it? :)

I had a similar problem. I think it has more to do with the higher protein in the greek yogurt. It balances out the sugar being absorbed too quickly.