I used to have that problem until I started setting the seams with the iron before opening them. Right after the sewing machine I press the seam and then either open it or fold towards the darker side. After that I press again. It takes a little longer to make a block, but the final size is more accurate and you will not need to worry later on about squaring it. This should work as long as your measurements were accurately done and the 1/4 seam is also very accuarte.
Maria