E-mails won't restore to original location

I have successfully backed up and restored e-mails, I am using Windows Live, Windows 7 64-bit, 6131 build. To test the restore I have tried deleting an e-mail from the inbox, but not the delete box. After restoring, the e-mail does not appear in the original location, which was the inbox. If I delete the e-mail from the inbox and the delete box, when restoring, the e-mail does appear in the inbox. I can't remember whether version 11 had this problem. I previously had trouble backing up e-mails, the problem was Windows Live was running while attempting the backup.