After upgrade, we get a PHP error stating the file not found, although it exists.
If we switch back to 4.1 it is fine, with no error.
I.e a script in /home/user1/public_html/ is trying to access a file in /home/user2/public_html/ - works in 4.1, but not in 4.1.1.
Permissions are correct and user is allowed.
Looks like some chroot is being enforced, even though it never has had a problem before.