Well thanks to BlueSup I managed to fix the issue myself. Thanks Skoda dealership...

The pictures you included reminded me to check that menu in personalisation for key assignation. I'm not sure if the software has changed in that there no longer is the option for seats in the personalisation menu directly as shown in the manual and on a mates Octavia but it appears that you don't need to select it there any longer. The seat was working on my key when I got it back but when my wife used her key it only gave the option to change the driver on the console. Once she did that everything moved to her settings.

Basically I selected her user then went into the driver two setting (her user) and scrolled down to where it said key assignment manual or automatic. I left the setting at manual and pressed the button which asked to assign the key to that user. It then popped up to ask me to press a button on the remote which saved and that was it! I still think the dealer did something as I'm sure that didn't work before but if be interested to know if it works for others or they need to update software them it'll work?