The waviness probably comes from having the binding fabric stretch when you sew the second side. If you think of a straight line running across your binding, if one end of the line on one side of the quilt gets sewn down beyond the end of the line on the opposite side of the binding, the binding will not be evenly turned and you will get ripples or waves. Clear as mud? Here are the techniques I use to get perfect machine binding.
(1) I do not cut the edge of the quilt. I mark the "virtual" edge of the quilt with a permanent marker, and use this line as if it were my cutting line. This helps for a variety of reasons.
(2) Starch the binding fabric before cutting, especially if the fabric was pre-washed. It doesn't have to be terribly heavy starch; even simple spray starching helps. It helps the binding not stretch while you are working with it.
(3) I do not press the binding in half. It seems counter-intuitive, but binding actually works better if you do not press in half. The reason is because it rolls better over the edge. I did not believe this until I tried it.
(4) I don't always use a walking foot. Having a "virtual" cut edge instead of a real cut edge makes the edge easier to control whether using a walking foot or not.
(5) Binding goes on top when sewing, for obvious reasons. I hold the binding up above the quilt sandwich and keep it nice and taut while sewing. This ensures that I do not sew more binding than necessary to the quilt sandwich. It's better to have more quilt than binding, so let the feed dogs gather the quilt while sewing to the taut binding.
(6) After machine sewing the binding on one side, I take it to the ironing board and iron the binding away from the quilt sandwich. You would not believe how much this helps!
(7) At this point I can cut the quilt sandwich down to size. Be *very* careful on corners; do *not* cut through the binding at corners. I mindlessly trimmed the binding at a corner along with the quilt sandwich and ended up with holes in the binding.
I experiment a little before deciding how wide to cut the quilt sandwich, testing to see how much I need to cut in order to get the binding to roll and be full without being over-stuffed.
(8) I go back to the ironing board and use Elmer's white washable school glue and my iron to glue-baste the binding to the right side of the quilt. This allows me to secure the entire binding evenly along the edge. It takes a little time but, when I take the quilt to the sewing machine, the final sewing goes much faster because I do not need to struggle with the quilt making sure the fold is accurate.
(9) I like to use a decorative stitch on the right side of the quilt. It helps a *lot* if you can choose a decorative stitch that does not have a center line. Too dense a decorative stitch will make the stitching very slow. My favorite so far is a feather stitch that does not have a line down the center. This website shows a lot of machine feather stitch variations that do not have the center line:
http://loopylace.com/anniescrazyworld/?cat=16 . My old Bernina 1230, which I love, does not have this kind of stitch. Its feather stitch goes out to both sides of a center line. The problem with center lines is that any deviation from the edge of the binding shows. With the decorative stitches that do not have a center line you can go faster and small deviations do not show.
Hope this helps!