I do mine like Bonnie Hunter from
http://www.quiltville.com
I lay out my quilt, layout the border fabric in the center of it, smooth it down and cut off the extra. If it is longer than my table, I pin it every so often so it doesn't shift, then I fold it up a bit at one end until the rest fits on the table, then finish smoothing and cut off the extra. What she says is that measuring tapes don't drape the same way that the fabric does. I've been doing mine this way for a while and I never have wavy borders. She's got a "printer friendly" version of the instructions on her website. Here is the link:
http://quiltville.com/borderhintspf.html