if you packed them in the most efficient way possible, i think both would have an equal amount of empty space. i just looked it up on wikipedia, which says that the greatest density occupiable by the spheres is 0.74048 http://en.wikipedia.org/wiki/Close-packing_of_spheres
that's a constant, so the volume of empty space is constant as well
say the jar is packed with 1 inch balls, and that 0.26 of the jar is empty space
if you were to magically double the radius (or diameter) of the balls, the volume would be increased 2*2*2 = 8 times
only 1/8 of this new volume would fit into the jar
and as for the empty space, the new total empty space would be 8*0.26 of the jar, but that doesn't fit in the jar either, only 1/8 of it does
so 8*0.26 * 1/8 cancels out to give 0.26 again
thus, still 0.26 of the jar is empty space
note about comparing with sand: even though you can't see it, there is a lot of empty space in sand. you know how easily water can fit in sand? there's lots of tiny spaces in there, and it probably would give the same amount of empty space as 1-inch balls