If you have moved media files around (e.g. put some in subfolders) then they will not be copied. You will need to manually copy the subfolders to the new media folder. Much easier to do this outside FTM rather than using the dialog box to find and copy or link the missing media.
If you decided to import from a backup file be aware that FTM appears to create thumbnails as the media items are used. Initially it will be very slow to scroll through the pane in the media view. Once you have shown each thumbnail once everything will speed up. (2014 shows thumbnails on the sources in the person view - this view will update slowly if you haven't seen those thumbnails before, so it is well worth spending a few minutes gradually scrolling through all your media items after restoring from a backup file).