I'm a longarmer so when I get wavy borders on a customer quilt, I'm kind of stuck with them! I have had success with steaming them heavily with my cordless iron and shrinking them up some. I have also had some success with using spray baste and evenly distributing the waves and smoothing them to the batting. But the BEST thing to do is fix it befor quilting it. I like the suggestion given to measur through the middles and less subtract 1/4".
I recently finished a BOM, Stitchers Garden and there were multiple border pieces, one of which was 4" embroidered squares! I knew this spelled trouble and I was ever so careful...I even cut all the solid borders on the lengthwise grain! But guess what? Yep...I had some wave! I used the above tricks and managed them but they can truly be frustrating and amazingly invisible until you're quilting the quilt! Best of luck to you getting this resolved.