I've never heard of a case where we didn't copy a file, Terrence: we don't treat dot-hidden files any differently than any other (though the globbing-match rules for scripts are a bit different, as you might expect).
Are you certain you did "Backup - all files" and the file was there on the original?
If you could send a copy of your SuperDuper!.log (in ~/Library/Logs) to support, I'll take a look and see if I can find anything unusual in there. An ls -la of your home on the original and the backup would help, too.
Thanks!
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--Dave Nanian
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