Seems there's a bug in the duplication process where only one of the variants was being stored as a term relationship. I've found a fix to this and have submitted a pull request via their GitHub repository: https://github.com/wp-e-commerce/WP-e-Commerce/pull/644
Here's a link to the (really simple!) patch: https://github.com/KZeni/WP-e-Commerce/commit/0ca11450b85858d791b18c8a2aa5e3ec9227a0a2
Essentially, you just need to go into
wpsc-admin/admin.php, find where it calls wpsc_duplicate_children() within the wpsc_duplicate_product_process() function, and move that to be before wpsc_duplicate_taxonomies() and wpsc_duplicate_product_meta(). Turns out the duplicate children process messes it up.
That's it! The terms will be duplicated properly, and that means the variants should be shown.