ajax_view.js backward compatibility breaks pagers

I've created a panels mini panel with 2 of the same views panes, but with different arguments.
The pager element gets set to 1 for the first view, and 2 for the second view.

ajax_view.js somehow gives both views the same set of settings, resulting in both views using pager element 1.
Below is the offending code:

      var view = '.view-dom-id-' + settings.view_dom_id;
      if (!$(view).size()) {
        // Backward compatibility: if 'views-view.tpl.php' is old and doesn't
        // contain the 'view-dom-id-#' class, we fall back to the old way of
        // locating the view:
        view = '.view-id-' + settings.view_name + '.view-display-id-' + settings.view_display_id;
      }

Removing the Backward compatibility part (the whole if statement) fixes the issue.

The issue may lie a little deeper, though, since the Drupal.settings.views.ajaxViews shows that there are 4 views (while there are only 2). It assumes view-dom-id-3, view-dom-id-4, view-dom-id-5, view-dom-id-6 exist in the HTML, but in reality only view-dom-id-4, and view-dom-id-6 exist.

Thus, when trying to find view-dom-id-3 and view-dom-id-5 it can't find them and tries to use the backwards compatility code instead.