if (defined $referenceTable{key} eq $systemKey) {
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I don't believe you want to use defined that way. Here is a simple demonstration why:

use strict;
use warnings;

my %referenceTable = (me=>5, you=>2);
my $systemKey = 5;
for my $key qw(me she) {
    if (defined $referenceTable{$key} eq $systemKey) {
        print "$key if\n";
    }
    else {
        print "$key else\n";
    }
}

__END__

me else
she else
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You probably would have expected to see "me if".

You should use strict and warnings to catch typos such as $referenceTable{key}, which probably should be $referenceTable{$key}.