Hi akaber,
Thanks for reaching to us and appreciate your patience.
1. I kindly recommend you to use WOODMART WooCommerce Layered Nav
filter instead.
2. Try to regenerate Regenerate the product attributes lookup table
in Woocommerce > Status > Tools https://take.ms/LGpvf
In addition, please check Woocommerce > Settings > Product tab > Advanced tab and disable Use the product attributes lookup table for catalog filtering
. Also, please make sure you added variable products and check again.
3. And Can you please check how the checkout works with the default WordPress theme and Woocommerce Storefront theme just to check whether the issue is with our theme or not.
Best Regards,