Sorry, I mistook line 71 for a similar looking line (the one in the foreach $intersect (@uniq) loop.)

If this is where you problem is:

my $refarray3 = $matchedfiles[5];
print "File: ${$refarray3}[0] in directory ${$refarray3}[1]\n";
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I'm trying to pass two elements per row. The filename and the MD5 value.



print "\n\n";
my $refarray3 = $matchedfiles[5];
print "it's not defined!\n" unless defined(${$refarray3}[0]);
print "it's not defined!\n" unless defined(${$refarray3}[1]);
print "File: ${$refarray3}[0] in directory ${$refarray3}[1]\n";
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Both of the elemnts in the 5th row of the matchedfiles array show the output of not being defined. It seems as if nothing is being passed to the array, when back on line 63 I have the following:

push(@{$matchedfiles[$c]}, [${$refarray1}[0], ${$refarray1}[1]]); I've updated the main post with the latest code.

Maybe that statement is never getting executed when $c is 5 - it's in an if statement after all. What's so special about 5?

You should just dump the entire @matchedfiles array to see what you have:

use Data::Dumper;
print Dumper(\@matchedfiles);
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