The electrics may not recognise manually adjusting it to the full open position. Try opening the boot lid to the max position either with the drivers door switch or preferably the keyfob. Keep holding the button for a couple of secs whilst its fully open.

Not saying it'll work, but that's my best guess.

 

Further to my previous reply, the following video may be of interest to you - check out from about 16min in to the video of the Octavia. Presenter seems to do exactly what you were doing, sets the hatch at lower height then manually pushes back to full opening, sets the system and it returns to full opening.

Dunno what to suggest.

 

:lol: If you can't manage to get it working with the suggestions above go to your dealer. My '17 reg was a pain in the a*se.
The boot lid had a mind of it's own. I ordered it Dec '16, even before the line started running, so that and other faults I suffered was the price I paid for being an early adopter.
They should have sorted ot by now.
So hopefully the tips above will work. It's another case of Skoda having a solution to a non existent problem, something of which they are very fond, making the cars over complicated (as do all manufacturers these days) with lots more to go wrong.
YES I admit, I AM a LUDDITE! :lol: