Take a look at the TreeList/Client-side Selection
online demo. If you first enable the multi-row selection checkbox and then select some of the child items of the parent row; you will see the label updates with the number of children you selected. But, when you subsequently collapse the parent, the label shows the selected items count as 0. Expanding the row a second time shows that your selections are preserved.
So, it looks like you'll have to first be certain that the parent is expanded prior to attempting to get the selected items after submitting the form.
You can reference this forum post for help in preserving the expanded state of the tree in session: Maintain State Between Callbacks?
Hope this helps!