Fabric and thread affect your 1/4" measurement. If you use thicker or thinner thread, different fabric, like homespun or flannel, this all affects your measurement. If you get a 1/4" foot and it makes the perfect seam for you without having to move the needle, you lucked out! Normally, you also have to adjust your needle position.
I usually use the same weight fabric and the same weight thread for all my projects but if I change something, I recheck my seam and move the needle if necessary. Here's a good tutorial on checking your seam:
http://www.quiltingboard.com/tutoria...ce-t89997.html
I also use a stiletto to guide the seam at the end.