If you measured through the center of the quilt lengthwise and crosswise and cut BOTH borders the measurement you got, you should have a very flat quilt and the longarmer, (I'm one too) shouldn't be putting tucks in your border. I recently finished one for a new customer that had wavy borders but since she told me to do the best I could, I did and will be hopeful that she loves what I did. An e2e pattern that has lots of back and forth motion which helps suck up extra fabric. A tight meander will be the best way to handle the waves if you don't waant to remove the border and do it right. Many people cut each border separately and cut off the fabric when they run out of quilt top. This rarely results in a nice flat quilt.
Judy