Odd behavior on swept 2D contour path

I am currently working on the CAM for a radius molding. The molding was created using the sweep tool with a profile sketch and a path sketch. When I try to do a 2D contour operation to clean up some sharp corners, one works as I expect and the other does not. See below:

As you can see, the lower path works fine but the upper treats the radius bit as a bunch of small sections that are not connected. Here is a closeup:

Has anyone ever had to deal with this before?