This is a limitation in OnDemand right now, where large downloads will fail to complete in one go. We have a bug report open for this here.
To work around this you can use the following command on a linux system:
wget -t 0 --user="MYUSER" --password="MYPASS" https://example.atlassian.net/webdav/backupmanager/Application-backup-20130509.zip
or use an addon such as Firefox' DownThemAll
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