Recently had to replace this regulator,and for some strange reason it is failing to work once the panel has been put back on..When the panel is off it goes up and down without fail so its not the motor any ideas on why this is happening...

It is an octavia ambiente

I'd think you must be dislodging the connector when refitting the panel. Try all the other electrical gizmos on the driver's door before and after too to try and narrow it down a bit.