I just downloaded node.js and virtualbox, when opening the downloads doorhanger after a while no downloads where shown. The downloads window, opened via "Show all downloads", listed both files as "File moved or missing" and "Show in Finder" was greyed out in the context menu. I first assumed both downloads had failed, but checking my downloads folder they both had been successfully downloaded. I ran both installers and they were working fine.
Do you have any add-ons installed? Does this happen with a new profile as well?
Just tested it again after restarting with today's Nightly update and it worked fine. Tried with the Node.js installer. Closing this and will keep in a eye on it in case this comes back.