I am seeing the same issue as described in https://www.drupal.org/node/2421645 with menu_block. However the solution isn't working. After a little investigation I discovered the reason I am seeing this is being introduced from the patch applied in http://drupal.org/node/2567875. If I change the FALSE value to an array in the call to menu_tree_prune_tree in menu_tree_block_data it seems to work for me. Patch to follow.