Just a thought here: I wonder if the waves are more noticeable when, in sewing the border to the quilt body, the border is on the bottom or the top. I would think that unless your machine has a feed equalizer feature (I forget the proper name--maybe continuous feed?) then the bottom fabric would tend to be pushed through at a greater rate than the top fabric, due to the feed dogs pulling the bottom fabric through. Thus you would tend to get waves on the bottom fabric. Maybe.
I have found a method that works for me, kind of the lazy girl's method. I just cut a length that I know is plenty long, and lay it in place on top of the quilt edge (which has been staystitched at the edge), on a bed or other flat surface. I very gently smooth the two fabrics together, not pulling or easing at all. Just lay one on top of the other, making sure each is flat. Then I pin, every few inches, to make sure there is no stretching on either piece. Maybe every 4 inches. Then sew. Any little stretching that the presser foot or feed dogs create (or natural stretchiness of the fabric that is cut WOF) will be eased in before you get to the next pin. This has worked for me. No waves.