I have the same problem. Although specifying the Page Layout in the Custom Design of Manage Categories will do the trick, the problem will be continue on my sub pages like the Product View pages which still uses the 3column layout instead of the 2columns-left.
I check my etc/config.xml and it do not have this line
<block type="page/html" name="root" output="toHtml" template="page/3columns.phtml">
I not sure if this apply to new version of Magento. I like to ask where in the etc/config.xml should I insert the above setting?