First, make sure that you ‘Lock In' your selection. If you do not do this, the Modifiers will not be applied. You can lock in your mods by pressing the triangle button in the Carcosan Modifiers menu.
Make sure that the Mods you have selected keep the screen in a “Balanced” state. If you have too many Protection Modifiers and not enough Trial Modifiers, you will not be able to Lock In your selection.