The grooves are to enhance the sealing. I rebuilt my master cylinder also and it was always my practice to put the grooved side of the washer toward an ungrooved surface. The grooved steel or cast iron surface will dig into a copper or brass washer and the grooves on the washer will help seal on a surface with no grooves.
I have seen it done both ways, flat to grooves or flat to flat, and it still sealed. Actually, copper washers will seal better than brass because they deform easier. I would suspect your washers are copper.