This sounds a lot like a Front Tonneau or Roof Position sensor problem. A Tech 2 will confirm. A Re-learn with a Tech 2 might fix the problem if the sensors aren't loose or faulty. 
One of the key concepts related to troubleshooting the Folding Top system is knowing the order of the opening and closing sequences. When a step fails, the problem is often associated with the failed step or in many cases, the previous step. 
The first step in either sequence is the windows have to be lowered. Indexing the windows stores their raised and lowered positions. If they aren't indexed, the next step (raising the Rear Decklid) isn't going to ever happen since the Folding Top Control module can't verify the windows are in the lowered position. Raising the Rear Decklid via a dedicated switch (on the dash or locally on the Rear Decklid) will still work whether the windows are indexed or not. (This is another trick to isolating Folding Top-related issues.) 
In this case, the Front Tonneau raised as commanded, but the Folding Top did not. If the Front Tonneau sensor is out of tolerance, the next step in the sequence (the top moving) is halted by the Folding Top Control module. The module will not initiate the next step in the sequence until the requirements for the previous step have been fulfilled. The control module raises the Front Tonneau to what it thinks is the Raised position, but because the received (actual) values from the position sensor don't compare to the stored values, the sequence stops. 
It isn't enough that the Front Tonneau raises. Its received sensor values have to be within the band that was committed to memory when the last re-learn was completed. A Re-learn is nothing more than a nominal Folding Top opening and closing sequence in which the sensor values are measured, written, & stored in memory within the Folding Top Control module.
This isn't the only condition that will stop the sequence at this point, but it's the most common.
Mod: Can this thread be moved to the Technical Discussion section please?
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