Did you manipulate the URL for Outlook.com to allow you to view your sms message online?
Like mentioned in
http://forums.windowscentral.com/win...p-outlook.html
If so, you've moved all of your SMS messages away from where they should be. To restore them on your phone, move those messages back again then use Outlook.com without changing the URL (so SMS messages are invisible) and run the backup steps again.
If your SMS messages weren't visible in Outlook.com, I don't know what the issue is. I've run through the same steps myself and have all my SMS messages. I've not seen anyone else report this same issue except when they've forced the view of SMS messages in Outlook.com.
And, is the date/time set up correctly on your phone?