If a file fails to show on the desktop, try clicking the desktop (left) to ensure selected and press F5 on the keyboard. I mimick F5 on the keyboard with a mouse stroke ("easystroke") and regularly "draw" a 5 on my desktop to get a file to appear on the desktop. I think it may either be a failure of Nautilus in refreshing or possibly nautilus crashing (do you notice any open nautilus windows "dropping out"?); nautilus handles displaying the desktop in Ubuntu.
Originally Posted by ihatetryingtopickaloginna
If crashing or seizing of nautilus occurs you can use command box, ALT + F2 from the keyboard makes it available, and the codes.
to quit any open nautilus windows, desktop icons will "dissapear" when this is used.
opens nautilus, thus desktop icons appear, but with no open nautilus window.
Or try stringing the 2 together to form a reset command (if nautilus is already crashed a reset won't work, but "nautilus -n" will),
should quit any nautilus windows, including showing the desktop, then restarting just the desktop, showing it's icons etc.
nautilus -q && nautilus -n
Your rebooting seems to have reset nautilus.
Hope this helps in future, Cheers.