I was running into this problem but it was with lightbox. What I did was change the paths that WP Shopping Cart is referencing to the plugin folder for lightbox. For example in the file wp-shopping-cart.php on line 903 it says:
<link href='<?php echo $siteurl; ?>/wp-content/plugins/wp-shopping-cart/thickbox.css' rel="stylesheet" type="text/css">
change it to:
<link href='<?php echo $siteurl; ?>/wp-content/plugins/thickbox/thickbox.css' rel="stylesheet" type="text/css" />
I can't tell you everywhere to go for thick box to change it to the thickbox plugin, however if you want to change it all to be lightbox you can change all by changing the class and rel in the product_display_functions.php file as follows:
around line 200 and 441:
a href='".$image_link."' class='ngg-gallery-thumbnail' rel='lightbox'
It was a bit annoying to find this with wp-shpping-cart. Too bad there didn't seem to be a simpler way. I'm on a mac running leopard so I can do a file content search directly from the finder. If you can do this it will help immensely. If not you may have to open all the files to search for this. Of course do not change any code without backing up your current wp-shopping-cart plugin just in case.