If the cup doesn't sit at the same height as the original, it probably isn't a correct match. There's always the chance that you installed the retainer upside down so double check that if there's any doubt before writing the cup off.

Assuming the cup isn't a correct match, it may or may not work properly with your cone, and different size balls. From time to time, I've run into questions of cup/cine/ball compatibility and resolved them by determining the ball track as follows. Clean and dry all the parts, and paint the races with a dry marker or die-makers blue. Assemble in your hand, or on the bike and spin the parts dry so the balls leave a line on the races. If the line is well placed on both cup and cone it's a pass.