Windows 7 won't restore backup data

I am writing for a friend who has 2 64 bit systems that were Windows Vista. He did a full backup on each system on an external drive and then installed Windows 7. On the one system all the files worked and the data was fine. On the other one, Windows 7 will not recognize the programs and nothing works. He ran the compatibility program prior to the install and there were no program issues. But nothing will run and Windows 7 does not recognize the system backup and allow him to restore. Has anyone encountered this? Any suggestions. :cry