I have two solid bodies that share a common surface. When I "Combine" the two, I get a patchy surface. Why?

As an aside, I also have a mysterious pink line. I didn't put it there, my references are hidden, and I have "Hide All Types" selected, and it does NOT appear in the assembly it is installed in. EDIT: After rebuilding a loft, the line went away. It turns out pink is the color edges turn when selected for Rotate View. I'm guessing this was an artifact of my crummy GPU - I have a history with this GPU and its general crumminess.

Thanks!