WooCommerce keeps showing variable products where specific variations are out of stock

I made a WooCommerce store that sells underwear. Almost all the products are "variable", and have different sizes (Small, Medium, Large, X-large).

Known WooCommerce issue: When you view the page for a particular attribute term, it shows all the products that have variations with that term, even those products where that specific variation is out of stock.
The product inventory setting is set to "hide out of stock products from the catalog", but WooCommerce keeps showing products where specific variations are out of stock.

WooCommerce developers won't fix this issue for now, see:
https://github.com/woothemes/woocommerce/issues/7026
https://github.com/woothemes/woocommerce/issues/5840#issuecomment-50601474

The store uses WooCommerce (2.2.10) in combination with a bunch of plugins.

I really need some help meaning the following plugin: Wordpress Meta Data & Taxonomies Filter (http://codecanyon.net/item/wordpress-meta-data-taxonomies-filter/7002700?ref=realmag777)

The plugin works great, except when visitors searching by size, products showing up even if that specific size is out of stock.

Developer realmag777 has no time to look at this particular problem. I hope someone else can take a look and hopefully fix this issue.