It can take weeks or many months for such adjustments to take place. However, this does usually happen. If fiber is the problem, you may need to step back and add it in more gradually. Many people can tolerate cooked fiber better than raw, at least initially. Take it gradually, if this is the issue.
Humans are genetically programmed to be able to eat a very high-fiber diet. However, we're also programmed to exist on a wide variety of diets, including very low fiber. When you make a major change, you body will have to make a lot of changes in the amount of various enzymes and other factors it uses to assimilate the new types/amounts of foods. Also, your intestinal flora will need to adjust.
There are probably a few persons who lack, or have lost, the capacity to make such changes. But this is essentially a disease condition and would be pretty rare. Most bodies will adjust with time and patience.