I was successfully using this plug-in version 188.8.131.52 with Genesis Simple Sidebars version 1.0.0. When adding terms to my taxonomies and then editing them, I had previously been given the option to update both sidebars and secondary navigation. After updating, the option to add the custom sidebar is gone, but the secondary navigation option is still there. My system still works - what I had previously entered still links. And after I added a new term and saved it, it seems to use the custom sidebar used by my other terms in the same taxonomy.
Is this a fix for you, or for Genesis Simple Sidebars? Writing that author, too.