Hi Daniel,
It sounds like you are using checkboxes from the Forms toolbar in your cells, and then creating an Outline or Subtotals with those cells. I think the problem is: those checkboxes are Objects, and Excel will not hide them when the cells are hidden (that's why you see them all stacked together).
To solve this the way you are doing it, I think it would take some moderately complex VBA code. Instead of using checkboxes, you may want to consider using data validation in those cells, if possible. That way, your users can still click in the cell to change the value, and you won't have the checkbox issue.
If you upload your file, I can take a look and suggest a solution...