How exactly did you backup? A move might do this, a copy shouldn't.
I use xcopy (for copying), and never noticed this. I don't use iTunes either, but it;'s very unlikely it would give this message after such a copy.
The following links might help to tell Windows what you want:
It seems an easy fix to me.
I have a My Book external drive and I backed up my whole My Documents folder to the external drive, but now iTunes refuses to open unless the drive is plugged in. It's reasoning is that the My Music folder on the external drive is now considered the System folder My Music and it considers the one in My Documents as just some regular folder.
Is there a way to re-associate the My Music/My Photos folders in the My Documents as THE My Music/My Photos folders of the system? It's rather irritating to have to keep lugging this drive around.