> I copied my /home directory to Windows for safe keeping.
What exactly do you mean "to Windows"?!
> To restore it, I exited GUI (Do you have to exit?) and used the copy command to send the /home
> dir back to where it should be (as root).
If you have a mounted vfat file system and you copied files to it you will lose your ownership permissions. If you copy them back as root, they will be owned by root. And no, you do not have to leave the GUI, you can simply open a console (xterm, gterm or whatever) in X11.
tar'ing would be safer as Tinkster pointed out. But you should be safely able to restore the files. I believe Mozilla has an option for importing mail folders. In case you have worked with Mozilla when the files were removed, it will re-index its mail folders and not automatically re-import them. You will have to do that manually. But first "chmod user.user /home/user/ -R" your home directory