It seems the plugin is ignoring tax_status, here is a quick fix for those that encounter the same problem:
Index: trunk/mh-wc-table-rate.php
===================================================================
--- trunk/mh-wc-table-rate.php (revision 1469679)
+++ trunk/mh-wc-table-rate.php (working copy)
@@ -63,6 +63,8 @@
$this->enabled = $this->settings['enabled'];
$this->title = $this->settings['title']; // Shown in drop down and admin order screen
+ $this->tax_status = $this->settings['tax_status'];
+
// Save settings in admin if you have any defined
add_action( 'woocommerce_update_options_shipping_' . $this->id, array( $this, 'process_admin_options' ) );
add_action( 'woocommerce_update_options_shipping_' . $this->id, array( $this, 'process_zones' ) );
Enjoy!
https://wordpress.org/plugins/table-rate-shipping-for-woocommerce/