I think backing up desktops is a good thing, but I wonder why are you
backing up the System Object if you are only backing up the documents
directories?  How could you restore the System Objects if you don't also
back up/restore Program Files?

Also, have you considered turning on Subfile backup?

Have you considered expanding your window?  We back up about 450 desktops
(we back up EVERYTHING, not just My Documents), smallest have 4 GB hard
disks, most have 12 - 18 GB hard disks.  We let them back up during the day,
while the servers back up at night.