you say that you are sewing an accurate 1/4" seam. But you aren't measuring the actual seam, are you? We talk about a 1/4" seam, but you don't measure the seam, you measure the resultant patch and sew wherever you need to to get the patch to come out correctly. If you change your fabrics or thread, your seam may need to be changed. I check at the beginning of each project and adjust as needed. Here's how to check:
http://www.quiltingboard.com/tutoria...ce-t89997.html
the other things that can cause a problem are inaccurate cuts. If possible, use the same ruler for the whole quilt, or at least the same brand.
and finally check your pressing and make sure you are not ironing in a tiny crease in the seam.