The culprits are high fiber and sugars that are poorly absorbed. By "sugar" I mean "type of compound" and this has little to do with what people think of when "cutting out sugar." The latter is often referred to as FODMAPs these days for short. This blog gives a good overview of what that means (just the best reference I could find, nothing to do with the site's diet recommendations).

Some people just need to start with slowly introducing these foods, eating small quantities and building up to more as the gut adjusts. That's my recommendation for you. Some may be truly intolerant to one or more of these sugars—lactose intolerance and fructose intolerance are the most widely-known manifestations. Since you mention protein shakes, I'll also toss out dairy protein (whey or casein) intolerance.

You say you're on the second week of this. How much have you changed your diet? You listed a few things, but in exact terms what would you have eaten on this day three weeks ago, and what did you eat today? What does your "semi-normal" dinner look like? How does it differ from what you ate three weeks ago?

The gut doesn't like rapid change, but it will adjust. You may discover a previously-hidden problem with digesting foods and need to change your eating habits to adjust to that.