Hello,
Take our apologies for the delay in answering.
We have inspected your plugin and found some functions that make variations work only on specific taxonomies. For example: http://prntscr.com/1z60aap – as you can see register_taxonomy_for_object_type() works only for product_cat and product_tag taxonomies but it would be much better to have some filter or actions to make it work for custom taxonomies such as ‘brand’ is. Examples: http://prntscr.com/1z60vwp or http://prntscr.com/1z614gk.
Also, we found that such taxonomy limits exist in other places too -> http://prntscr.com/1z618jy (only for product_cat and product_tag taxonomies).
But good news is that you can make force recalc for brand with product variations -> http://prntscr.com/1z61csk ( they use default woocommerce filter for these taxonomies ) – but it does not make it work on ‘brand’ taxonomy anyway.
The next code http://prntscr.com/1z61r28 would be better to replace/improve with my version (or smth else more universal) -> http://prntscr.com/1z61z5v.
For more info about compatibility with custom taxonomies, please, contact with plugin’s author.
We did what we could for you.
Regards