Wasn't able to give this much attention over the weekend. Went down tonight to have a look and the seal was pretty much stuck to the roof :s Could hear the motor trying to do its job but it was really stuck on the roof!
Plastic bit seemed to be in the correct position and functioning properly.
Cleaned the edge of the roof where the cutout begins and put a light layer of grease in the dirts place. I've no idea how to actually lube the seal as it's always hidden...
After applying the grease, I put the glass in the closed position, then down, then up and down. Many times. Reapplied some more grease and did it again.
It now seems to be working as usual and I will keep an eye on it over the next few days to see if it continues to improve.
Thanks all for your help