Windows 7 Permissions - Windows rebuilt using default settings, now Windows not booting

I have a system that has 7 partitions that were working fine. Recently, my computer said that the permission files were damaged and the system ran for hours rebuilding the permissions using the "default permissions". Now, none of my partitions work.

The OS loader runs fine, I select any of the partitions and tell it to boot. I get the Windows splash screen with the 4color animated Windows logo. The system then goes blank except for the mouse curser. I can move the mouse. After about ~20 minutes, the system reboots.

Any ideas on how to get them back?