The developer community comes to the rescue. One effort that does what is needed here is called Déjà Vu (DV). DV is a preference pane that lives in System Preferences and allows unattended backups of folders onto the shuffle. It's $25 for a single user license. See Figure 1 below.
You can schedule the backups for a certain time, even when you're not logged into the machine. Incremental backing up of only the files that have changed since the last backup is also an option. Folders can be mirrored; that is, files that are deleted from the source folder can also be deleted from the destination folder.
DV is actually a program wrapper for the psync perl script written by Dan Kogai for his MacOSX::File perl module that does most of the heavy lifting of backing up files. No shame there because psync is as un-Mac in its interface as you can get. But unlike most Unix utilities, it understands the Mac file structure and doesn't mess with the Mac-specific attributes of a file. It makes copies of Mac files that are real copies.
Anyway, DV is a fine way to sync your files on your shuffle if you are comfortable with accessing a preferences pane.