Also remember that you don't actually measure your 1/4" seam, you measure the resultant patch. Here are good instructions:
http://www.quiltingboard.com/tutorials-f10/achieving-accurate-1-4%22-seam-allowance-t89997.html
The thickness of the fabric & thread weight affects where that pesky seam is going to be on your machine. It may vary from project to project, so it's good to check at the beginning of each project. Even with a 1/4" foot, you may need to adjust your needle position.
Also, starch before you cut your pieces!