Everyone has given good advice. The reason the border appears to be the right size at the seam line is that the feed dogs move the bottom fabric a little more than the top fabric. The difference isn't noticeable at the seam line, but it is at the edge of a border. Using a walking foot would have helped, but measuring first through the middle, cutting the border to length, and pinning it evenly across the quilt would still have been the best way.
Several options have been given to you. I think the best one is to take off the borders and reattach after cutting them down to the correct size. This sounds like a lot of work, but in the end you're fixing the problem rather than trying to deal with the aftermath. Unfortunately I don't know if you can do this after spray basting, since I have never done that.