[cflsystems]

You said calling

<link rel="stylesheet" type="text/css" href="{$SkinDir}/lib/colorbox/colorbox.css" />
<script type="text/javascript" src="{$SkinDir}/lib/colorbox/jquery.colorbox-min.js"></script>

will still not load it if js/css tool is on? This doesn't sound right. It should load just fine - these are direct calls and have nothing to do with cache. Have you tried putting it in home.tpl just before </head> and no ifs. Look in the sourse code if it's loaded, no matter if it works or not.
By the way if you are calling it from product_details.tpl there is no need for the if statement - that IS $main = product