If you are trying to set a new position that is lower, press the open tailgate button from a closed position, then press the button once to stop it where you want it. You can then manually move it up and down if not quite in the right spot. Then you have to wait at least 3 seconds before touching the button again. Then press and hold until you hear a long tone.
If you are trying to set a new position that is higher than the one currently programmed, after it stops, push it farther up manually until it is in the desired position. As before, wait at least three seconds, then press and hold until you hear a long beep.
I'm guessing you are not doing either the 3 second wait or not pressing until you hear the long tone.