It should click into place, are you talking about the hatch portion or the actual lower tailgate?

If its the upper piece, there are little rubber buffers on the sides of the hatch that you can screw into the hatch farther, sometimes if they are out too far it prevents the hatch from "latching on"


And what color is your 6 speed manual? I would have killed to find an 06 back in the day, please post up in the manual transmission registry to get you registered and show some pics!

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2018 Ram 2500 6.7L Cummins 68RFE
19k miles -Bright White/Black - Big Horn Sport - Crew Cab Short Bed
2013 X5 35D (CEO's) - Born on 5/17/2013 -
82k miles - Alpine White/Cinnamon Brown/Premium Pkg, Sport Activity/Premium Pkg and Sound/20" Style 214/Running Boards