If your patchwork blocks are larger than the plain ones then you either cut the small squares too large or the large block too small OR your seam allowance is off. Here's a way to check:
http://www.quiltingboard.com/tutoria...ce-t89997.html
As far as proceeding on this quilt, how much are the blocks off? You have some options. If the blocks are off a small amount, like 1/8", you can ease them. Try putting the larger block on the bottom against the feed dogs to ease the excess.
If the patchwork blocks are too small (and were cut correctly) the seams are smaller than 1/4". I would tug on the seams a bit. If they are sturdy with the smaller seam, you have the option of just trimming them down to 9.5", taking an equal amount off opposite sides. If the seams pull apart, you will need to take them apart and re sew them.