I support a lot of Macs and it’s much easier to work on them remotely via SSH to do things like permission fixes, ACL repairs and other sneaky things. Here’s how to repair permissions from SSH/Terminal:
diskutil repairPermissions /
Of course you may need to sudo or use the su command to do this.
You can also do a repair disk this way too but that may dismount the users active drive so use with caution:
diskutil repairdisk /