If my blocks were that little "off" (and mine usually are!) I would just ease them in, as mentioned above. I don't square up every element of every block and do try to square up big blocks, but, like you said, same machine, same thread, etc, and they are not always exact. And somehow when I am done with the quilt it is pretty much square, just needing a bit trimmed here and there. I can't figure it out either!!