It could be your "improved" diet. There are some things that are generally healthy, but your body doesn't tolerate them. I rarely eat processed foods, for example. I cook from scratch every day. But I cannot eat chick peas or palm oil because they both give me Irritable Bowel Syndrome. Palm oil is in most processed baked goods, ice cream and chocolate, as well as most peanut butters. So it encourages me to avoid processed foods, and I am really careful about peanut butter (only good old SunPat for me).
So it could something like that for you. For example, nuts and seeds generally are considered healthy, but they really are hard to digest for a lot of people.