I have run a Backup-spsite and then a Restore-spsite from a development farm to a production one. The permissions set on the development farm have not been carried to production.
The site collection admins were not set correctly. The site collection permissions were set by no to the correct user:
Instead of domain\username it was recorded as i:0.w|domain\username.
When assigning people permission they do not seem to work. Users who had perms in the last site now have two entries in the select user list.