You're certain that the first file is actually opened? I see that you don't check the status of 'open' with something like this: 
open(my $csv, "<", $file) or die "Unable to open $file: $!";

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Update: Original OP's post did not include "use autodie"

In reply to Re: Performance oddity when splitting a huge file into an AoA by roubi
in thread Performance oddity when splitting a huge file into an AoA by Xenofur

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