If this problem doesn't go away, you may have a position sensor or switch issue.
When a sensor value doesn't match what's stored in the system's memory, the Folding Top will not advance to the next step. This is a protection measure because the system doesn't know the position of a component. In your case, the Front Tonneau folded up, the rear deck lid raised, the Header Latch should open and then the operation stopped. The next step is for the Rear Tonneau to retract.
First, inspect the physical mounting of the Front Tonneau position sensor; it's located between the seats at the front of the trunk behind the fabric cover. If it's loose, that will affect the resistance value. Ensure the Front Tonneau isn't mechanically binding and is moving to the fully extended position, by manually moving it as per the Owner's manual instructions.
Next, check the physical mounting of the Rear Tonneau position sensor. It is located on the left/rear scissors lifting mechanism. You could unlatch it and re-stow it to move the sensor per the same procedure in the Owner's manual.
Running the cycle again with the Header Latch cover removed, you should see the hex head rotate as it opens. When it opens, it sets a switch to inform the Folding Top Control module it has changed position. The switch is pretty reliable, so I would be more inclined to believe this to be sensor-related.
If everything looks and operates mechanically, you can manually raise the top and lock it into place. You need a Tech 2 to examine the system in operation and perform a sensor re-learn if a sensor is out of tolerance or replaced.
This will likely mean a dealership visit if you don't have access to a Tech 2.
CCC
