This is, as others have eluded to, a characteristic of the Dado blade you are using.
In a normal situation, this is not an issue at all, as the Dado is hidden from view and the groovy bottom (for lack of a better term) does not affect the strength of the joint in any way. It can be an issue if the joint is exposed.
The simplest way to eliminate this problem is to simply purchase a higher quality Dado blade, such as those made by Freud, or Forrest, but they can be a budget breaker for sure.
In those situations where the joint will be visible in the finished product, there are a couple of methods you can use to achieve that flat bottom Dado.
The first method is to cut the Dado with a router and a straight bit. Use a bit with a smaller diameter than the final width of the Dado, and make two passes to achieve the width desired.
A second method would be to use the Dado blade to cut the dado, but cut it a little shallow by say a 32nd or 16th of an inch. Using a router with a straight bit, or a rabbet plane (such as Stanley #92), bring the joint to final depth. This has the advantage of having the dado match the width of others in the project, but will give you the look desired. This also has the advantage of not having to locate the edges of the joint with the router, as they are determined by the dado blade.
A third method would be to go old school on it, and grab a router plane and do it by hand. With a sharp bit, this isn't as difficult as it seems, and doesn't really take that much time at all. In fact, some people would probably say that this method can be faster than those mentioned above, and is much more satisfying.
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