OK, thanks for the additional information.
I've done some investigation, and it turns out that this is not actually related to theme compat at all (or plugins.php for that matter). The problem is that the sample plugin is not using the 'default_subnav_slug' parameter when registering the nav item with bp_core_new_nav_item(). If you do this, it works:
bp_core_new_nav_item( array(
'name' => __( 'SubNav', 'bp-subnavy' ),
'slug' => 'subnav',
'screen_function' => 'bp_subnav_screen_settings_menu',
'default_subnav_slug' => 'subnav',
'position' => 40,
'user_has_access' => bp_is_my_profile()
) );
This is kind of a quirk in the way that bp_core_new_nav_item() works. (See http://buddypress.trac.wordpress.org/browser/tags/1.6.4/bp-core/bp-core-buddybar.php#L87 to see why.) In the future, it would be nice to refactor this function a bit so that this requirement is not in place - there are other reasons to want to refactor this function anyway.
For now, this is not a regression, and it can easily be avoided by using the default_subnav_slug item. I'll update the ticket title appropriately. Could you please pass this along back the OP on the forums?