FWIW: I get your expected results. Albeit from slightly later versions of both modules: 

C:\test>junk11
Clone: 0.31 Data::Dumper 2.125
orig: 3 clone 3

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Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
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In reply to Re: Why does this combo of Data::Dumper and Clone::clone() fail? Bug? by BrowserUk
in thread Why does this combo of Data::Dumper and Clone::clone() fail? Bug? by Lightknight

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