Bean permissions with Workbench

I initially thought this issue was related to Inline Entity Form, but now I'm thinking it has something to do with Workbench. I've inherited a site with lots of customization regarding the Workbench that I don't entirely understand, so this may be related to my custom code.

I'm using Bean (7.x-1.11) and Workbench (7.x-1.2) and Workbench Access (7.x-1.4). I have an editor role that has access to specific content types via editorial access. If I give the editor the "Administer Beans" permission, they can edit all beans. I only want them to be able to edit "ABC" beans. I have permissions enabled for the editor for "ABC: Add Bean/Edit/View/Delete." If I remove the Administer Beans permission, then they can't edit ABC beans anymore (through Inline Entity Form or /admin/content/blocks) or Add a new block through the Inline Entity Form.

Is there some configuration that I'm missing or is it likely that my custom code is stripping out the permissions?

I did see this issue: https://www.drupal.org/node/2706463, and it sounds similar, but I don't know if it's a duplicate. In my case, the permissions don't seem to apply anywhere.

Thanks!