Windows Backup Missing Files

We recently had a need to replace a hard disk. Our original files were all backed up with Windows Vista Backup. The backup process produced no errors and appeared to complete successfully. However, when we restored the backup to the new hard drive, we found that there were many missing files. To this point, it appears that the missing files are all .EXE files. In many cases, all the files were restored to a folder, except for the executable (.exe). We know that these files existed when the Windows Vista Backup was performed on the original hard disk. Moreover, we backuped the same files later using a different program and have confirmed the files were there.

Is anyone aware of a problem where Windows Vista Backup is either NOT backing up all the files or is NOT restoring all the files? Furthermore, it is odd that this seems to have affected only certain files which brings us to wonder if our security software could have blocked files somehow without our knowledge