I just want to add my experience to the lot. I had similar issues using Drupal menu. The solution I used is:

- Set all menu items with children to "Expanded". This as to be done manually: ```Structure > Menus > List links```, edit links which has children, check the ```Show as expanded``` checkbox.
- Use ```menu_tree_page_data``` function (example: ```$menu_tree = menu_tree_page_data('main_menu')```) to get the menu, with all its children AND with active trail.
- Create a renderable array using ```menu_tree_output``` function (example: ```$renderable_array = menu_tree_output($menu_tree)```) to prepare the menu for rendering.
- Use the renderable array as content for my custom block, but you could call ```drupal_render($renderable_array)``` to get the rendered HTML representing the menu.