Bulk Generating URL aliases for taxonomy terms doesn't do anything
You'll need to troubleshoot your own site configuration to understand what's not causing the path update on the bulk form. If you look at the flow of execution, you can follow


The bulk update submission handler
The bulk update batch processor
The bulk updater


Ultimately, all the form is doing to update is using pathauto_taxonomy_term_update_alias_multiple() to load/save a group of tids in bite-sized chunks; if you fail to pinpoint the problem, you can use that function to do what you're already doing manually.