Site Restore Problems

I am attempting to restore an account from backup. It is the only account on the server. The file is around 11gigs in size and the restore seems to take roughly 4-5 hours to complete.

The strange problem I am having is that If I check the sites about an hour or so into the restore everything works fine. The most important sites all come up and seem to work correctly. By the time the restore finishes a few hours later however the sites no longer work. For example, when visiting one of the Joomla sites I get the plain, unrendered PHP code from the Joomla index.php file. Same thing for the magento sites. If I run the restore a second time the same thing happens. An hour or so into it the sites work fine, but if I wait another few hours for the restore process to complete then the sites go back to downloading the raw index.php files when going to the sites.

Any ideas of what troubleshooting steps I need to do to fix this?