if you got sugar water on the paper, they probably went though it pretty quickly. did you leave an upper entrance for the top box? Also, did one hive have stores and the other not? they might have just started robbing rather than combining.
i prefer to use an old window screen, or window screening. you can leave it for a couple of days and the scent mixes without the bees mixing. it means an extra step in removing the screen, but it seems to work well for me.