Non flush floorplates are a PITA Jack. I find it's mostly from improper removal, prying under the edges with a screwdriver or driving a punch down between the tables without removing all the floorplate screws and warping the plate. The floorplates aren't so hard that the can't be flattened again. I lay them on a thick flat block of aluminum, or bridge them between two blocks, and use a small leather or plastic hammer to gently bend areas that are warped. You can use a small metal straight edge and the surface of the block to gage for flatness where you perceive a problem and gently tap where appropriate to get it back to where it should be. Sounds like you've inspected it carefully for burrs. Once they're cleaned up you should be able to get it seating flat again. Just be cautious.
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