Category Tree

I have categories setup in my shop, but they don't seem to be working and I don't understand why ..

I have a main category with several subs

In the admin category tree I see the main plus the subs
I see that one of my subs has one item .. none of the others have anything

When I shop as a customer and click on Dept .. I see all my subcategories ...
I click on one I know doesn't have an item and it brings up items in another subcategory

Any suggestions would be appreciated

Thanks,
Nick