I have run into this problem before. The problem is in there is some code in the send_keys.php file that is causing every product to generate a key. I would personally just disable the module and follow this:
http://forum.x-cart.com/showthread.php?t=29161
X-Cart already has the code to do this, you just need to add it in. Open skin1/mail/html/order_data.tpl and add this code somewhere in the product listing (after the {foreach from=$products item=product} and before the next {/foreach}:
Code:
{if $active_modules.Egoods and $product.download_key and ($order.status eq "P" or $order.status eq "C")}
<br />
<a href="{$catalogs.customer}/download.php?id={$product.download_key}" class="SmallNote" target="_blank">Download</a>
{/if}