How big is the quilt? 1/4" off in places probably won't matter on a larger quilt. Are you sure this is going to make a difference?
Typically you would want to square up your quilt before adding borders, measuring through the middle of the quilt and cutting your borders to fit that measurement. Usually you do this for the side borders first, then again for the top and bottom borders. If you have multiple borders, you go through this process for each border.
Did you measure through the middle of the quilt and cut the borders before sewing them on? If you did not, then you may want to remove the borders and start over. This is because the tendency is always to sew on more border than there is quilt top if you do not pre-cut your borders. Even with a single border, this results in wavy edges on your quilt. The wave effect gets even more pronounced with multiple borders.