... I wonder if the script is timing out for you. If that is the case, there is a PHP installation variable (your hosting service should be able to help you with that) which defines the maximum execution time for any php script. With that volume I suppose you may be hitting the that limit (just a hunch as I've had similar problems with other plugins because of this).
(I'm sure there are developers here quite able to put it together... I might even give it a go when I get some free time)