If you are using a 1/4 inch foot and it isn't working, you might need to "calibrate" your foot. You do that by carefully cutting two pieces of fabric (I use 3 1/2 x 6 1/2 inch) and piece them together along the 3 1/2 inch side. After carefully pressing open, measure. You should have a 6 1/2 inch square.
The other issue could be you are using different rulers to measure and they are not accurate. I try to stay within the same brand on a project. It can make a big difference.