So, in the process of migrating my linux install to a VM, the permissions changed. Quite simply, I can't log into the system in question other than booting the vm from the iso image and chrooting after mounting the partitions.
The OS is Archlinux.
Steps that got me here:
1. rsync backup of the computer (excluding certain things)
2. Attempted to mount the drive I backed up to on VirtualBox. Didn't work at all
3. Created a new VM in Hyper-V and added the VHD and the physical drive
4. rsync restore of the backup to the VHD
5. Booted with VirtualBox
6. Reinstalled Grub, installed virtualbox guest additions (through pacman)
7. adjusted fstab and regenerated the initramfs (mkinitcpio -p linux)
8. exited chroot and poweroff.
9. Start the VM up again and attempt to log in
10. authentication failure and plain refusal to login as my user or root
11. Boot into iso, mount partitions, chroot, ls -l
ls -l shows all of the directories at / (except /dev /lost+found /proc and /sys) having rwxrwxrwx (777) which I assume is the problem.
lost+found has 700
the other three exceptions have 755