I agree, with a rail fence design you can trim and square up all your blocks and it shouldn't be a problem. I would go back though and turn the pieces over and measure your seam allowances. You'll quickly see if this is the problem or not. If you aren't sure, simply sew two pieces of 2 1/2-inch fabric together and iron open. It should measure 4 inches across. If it doesn't, then you can see whether you are sewing too much or too little of a seam.
There are several things that could be the culprit in a block not coming out the right size.
What is the thickness of the thread you are using? Belive it or not, the thickness can end up making a huge difference in the size of the seam and not all threads are created equal. The thicker the thread, the more we have to take it into consideration when sewing.
Make sure the pieces are cut exactly each time. If you are off even a sliver, which is 1/16-inch, then in just 8 pieces you are almost a half inch off. This can make a huge difference across the length of a quilt. Often this is my problem area. I'll cut several pieces perfectly and then measure one out 1/4-inch extra. :roll: Really messes me up in spots.
Ironing can also be a huge issue when trying to get blocks to come out the right size. I'm sure you've heard the quilting commandment, "Thou Shalt Press, NOT Iron!" :lol: It's true you don't want to scrub your pieces out of shape, but by the same token you don't want to press too lightly. Don't be afraid to really press the block. I know it probably sounds a bit strange to hear that but it does make a huge difference if done wrong.
I hope some of those things help. I think it's wonderful that you haven't let this stop you from finishing your quilt. Good for you! I can't wait to see a picture of the finished top.