So, you unlatch and put the top up. The windows go down. You press the button and it just beeps.

Possible causes:

1) The divider in the trunk is not deployed (obviously not the case) OR the sensor for the divider is defective.
2) The trunk lid is open (obviously not the case) OR the sensor in the trunk is defective.
3) You are going faster than 9 mph (obviously not the case).
4) The electric trunk lock is not working OR it IS working but it's sensor is not indicating to the control module that the trunk IS locked.

To restate 4) above:
Now, you say it beeps telling you it doesn't like something. Normally, the instant you press the button you will hear a soft sound from the trunk, it's the electric lock actuating so that you can't open the trunk during the 23 seconds the top is going up or down. I suppose the problem COULD be this mechanism is not working. If that electric lock does not activate and indicate to the control module that the trunk IS electrically locked, the controller won't let the pump start AND you will get a "beep" sound.

Do you hear the electric lock make a sound from the trunk when you press the switch? Or do you just hear the "I don't like something" beep?