Heather, I have been working on my Checkerboard Chain today. Yipee! I echo what Janice and SBG said. Basically, check your 1/4" seams and make adjustments. Also make sure you press your blocks from the back and from the front to make sure the blocks are really flat. If you have the clappers or something like that use them. Each little smidge of extra fold when you press the seam can change the final measurement of the block. The scant 1/4 in seam may be just the ticket. That means just the tiniest smidge off that 1/4 ", like a needles width. Good luck and keep at it. As you see it does look lovely when finished. Are you pressing seams open or to the side that can also make a wee bitty difference that can add up enough to make your squares not quite measure up.
I have 36 or 37 of the larger nine patches finished and about 10 of the smaller framed 9 patches. Hoping to get them all finished by tomorrow night and turned in to a finished quilt top. Fingers crossed.