I had this and got it 'fixed' at a main stealer for £300 or thereabouts.
It's down to the roof mechanism running out of alignment, or so they tell me...
Anyway, a year later the exact same problem started again
That's when I investigated myself - I can't afford to just keep throwing money at it, especially the way a main dealer mugs you. And nobody else near me will touch it.
With mine it was simply down to the 2 levers within the hood mechanism - one wasn't fully locking out to force the roof down that last few millimetres.
Have you tried this? You do need to give a firm push on the levers.
In my case I don't need to pull the manual release cable to slacken the thing off or mess with the locking bolt in the boot (have a look at your handbook), though this might not be the case for everyone.
My roof is very slow to move and I do need to give it a helping hand at various stages, but it's not left me in an awkward situation for a while now.
Spend some time messing with it, it was a bit of a eureka moment for me when I finally got mine working and it's given me the confidence to actually use the damn thing more