It is not completely clear to me what output you are trying to achieve (a small sample of the output you expect would make it clear), but perhaps a different approach using a different module (XML::Twig) could help you to avoid this problem. I realize this does not directly answer your XML::Simple question, but it is something you could consider.

use strict;
use warnings;
use XML::Twig;
use Data::Dumper;

my $xmlStr = <<XML;
<project by="company" name="personname">
  <pattern name="company-000001" owner="company" description="Microarr
+ay" species_database="d.base">
    <reporter name="A_24_P344666" systematic_name="NM_020341">
      <feature number="1780">
        <position x="0.733234841870825" y="10.033" units="mm" />
      </feature>
      <gene systematic_name="NM_020341" primary_name="PAK7" descriptio
+n="Homo sapiens p21(CDKN1A)-activated kinase 7 (PAK7), transcript var
+iant 1, mRNA [NM_020341]">
        <accession database="ref" id="NM_020341" />
        <accession database="ref" id="NM_177990" />
        <accession database="ens" id="ENST00000378429" />
        <accession database="ens" id="ENST00000378423" />
        <other name="accessions" value="ref|NM_020341|ref|NM_177990|en
+s|ENST00000378429|ens|ENST00000378423" />
        <other name="chr_coord" value="chr20:9466136-9466077" />
      </gene>
    </reporter>
    <reporter name="foo" systematic_name="boo">
      <feature number="1780">
        <position x="0.733234841870825" y="10.033" units="mm" />
      </feature>
      <gene systematic_name="boo" primary_name="goo" description="Homo
+ sapiens p21(CDKN1A)-activated kinase 7 (PAK7), transcript variant 1,
+ mRNA [NM_020341]">
        <accession database="ref" id="NM_020341" />
        <accession database="ref" id="NM_177990" />
        <accession database="ens" id="ENST00000378429" />
        <accession database="ens" id="ENST00000378423" />
        <other name="accessions" value="ref|NM_020341|ref|NM_177990|en
+s|ENST00000378429|ens|ENST00000378423" />
        <other name="chr_coord" value="chr20:9466136-9466077" />
      </gene>
    </reporter>
  </pattern>
</project>
XML

my %data;
my $twig= new XML::Twig(
    twig_handlers => { reporter => \&reporter }
);
$twig->parse($xmlStr);
print Dumper(\%data);
exit;

sub reporter {
    my ($twig, $rep) = @_;
    my $name  = $rep->att('name');
    my $sname = $rep->att('systematic_name');
    my $pname = $rep->first_child('gene')->att('primary_name'); 
    $data{$name} = [$name, $sname, $pname];
}  

__END__
$VAR1 = {
          'A_24_P344666' => [
                            'A_24_P344666',
                            'NM_020341',
                            'PAK7'
                          ],
          'foo' => [
                   'foo',
                   'boo',
                   'goo'
                 ]
        };
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