A few notes to keep in mind about the check-boxes and how parent items relate to child items:
Checking a parent item will check all of the child items beneath it.
Un-checking a parent item will un-check all of the child items beneath it.
However, if you check a child item the parent item will also appear checked, even though all of the child items are not checked. Glancing over the items it may appear that all of them are selected if you are looking at the parent items, however if the child items were selected individually you won't be able to tell a difference by looking at the parent item if all or only some of the child items are checked. If a parent item appears un-checked, though, all of the child items will also be un-checked.
Note: If by default a parent item only has some child items checked, the parent item will appear unchecked. Selecting any additional child items will automatically check the parent item box, even if all of the child items still aren't checked.