Re: Issue with Auto-Manage
When on the campaign map, push 'escape' to bring up the menu. Under 'game options' there is the line "always allow building and recruiting". Make sure there is an 'x' in it's box and the auto-managment option should now be changable.
Re: Issue with Auto-Manage
Because you have reinstalled M2TW the setting 'manage all settlements' is not on. If the above doesn't work you can start a new game and make sure that you have chosen to manage all settlements. Once you have played a few turns load your original save game and it should be as normal.