Seat Leon lost r 1st and 2nd gears

i have completely lost R, 1st and 2nd gear - 3rd is available by moving into reverse position, by pushing down across and up. 4th is available with a bit of effort, but appears like 2nd gear and 5th and 6th are easy to get to, but in the position of 3rd and 4th.
Seems like the gear box has shifted and is out of alignment

this has happened a couple of times before, but seemed to fix itself. It only ever seems to occur after using cruise control on longer distances. Short distances, there was never an issue and on longer journeys with no cruise control, never an issue - however in this occasion, what is different to the previous ones is that when in neutral, the stick is rigid and cannot be moved in the way you'd expect to be able too.

I should add that 1yr ago, I had a clutch replacement.
Could it be related in some way?