Color could be playing tricks on your eyes. You know how realtors use light colors in a room to make it look bigger. This is the same principle.
It could be that you are using the wrong mark on the ruler when you cut. If you cut on the inside of the line or right on top of the line, your block will be off. You always want to cut on the outside (waste side) so that your block is just a couple of threads bigger than the measurement. This will help compensate for the few threads that are lost when the seam is pressed. (Yes, it is a minute amount, but it plays havoc with your stitching.)
You have to be absolutely diligent about cutting the same way each time, and stitching an accurate 1/4". Take the time to determine where you need to feed the fabric to be absolutely accurate. A little time spent to get this skill down will pay you big rewards later on with less time spent unpicking.