Rounds have a tendency to do that because they need to make true rounds and match tangency. 1st suggestion would be to create the rounds in the blended sweep sections. The section where the rounds quit can be done with a boundary blends between two segments.
These are always a challenge. Rounds in particular prefer to be curvature continuous for most ID people, but that can cause other issues in the software. It all comes down to a gentle art of persuasion in the software.
You're on the right track. And in general, those mismatches on the radii are not an issue in manufacturing. If this causes a problem in your analysis software, you might forward your model to their customer service group to see what they cannot handle what is quite basic geometry.
