So according to members on another forum (BritishExpats) its not unusual for the upload section to not appear and for the system to not update your application properly.Have found this webform http://www.cic.gc.ca/english/helpcentre/answer.asp?qnum=1311&top=23 to use. Will wait till next week and try to make contact too.
The advice is to send everything via post and a note explaining that the online system have an upload section. (photos, photocopy of the bio page of your passport , and a copy of the PPR email with the end bit filled in (eye colour etc)).
I'm going to drop mine off Monday, if they don't accept it I'll post it in the closest post box.
edit: its not necessary to raise the technical fault but I think its a good idea if we both do, maybe they#ll actually fix it.