I found what I had done wrong. The rabbet and dado are 0.125" wide. That is exactly the width of the tool. However I had it leave a small amount for a second pass. So how could the rough do anything if the tool is wider then the rough width.
Ignore the rest of this!
Most of the inside is rough routed just fine. Two dado are not routed unless I use “outline” without checking inside only and outside only. If either box is check it is not routed. See image. Since this is a registered part and will be flipped it is not a good idea to route the “outside”.
So there seems to be an issue with the operator. 