By default you can not enable or disable with the Tree checkboxes, you need to select the Fx you want to modify and click the Enable checkbox in the Fx edit zone.
You may want to allow Enable/Disable of Fx by clicking on the tree text or checkboxes, but it is recommended to not let this always active as you may enable or disable Fx by accident just by browsing thru the tree.
Tip : If you have many effect to enable/disable you can use ⌘ + Click to select several Fx and then use the Enable or Disable Menu by a right click on the Tree.