Are you running the exact same code in both cases?. Your output looks like you called $conf->getall in scalar context before assigning the result to %config. Something roughly like : my %config = scalar $cong->getall;, except the problem is probably far less obvious. But then you should have two warnings if they are on:

Odd number of elements in hash assignment at - line X.
Use of uninitialized value in print at - line X.
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