I tried to replace my level highway connection with a elevated highway connection and I had some issues trying to get them connected properly.
But I recently noticed that the highways aren't connected and their is a bug where all the roads look like highways in the two cities in the region.
You can clearly see the difference in this screenshot: http://cl.ly/image/0w0O1L2j0b1s
I have also attached the screenshot below.
I am using the latest NAM. But nothing else on my Windows 7 machine.