Looking at this in the debugger it seems that XMLin() may not be giving you what you expected:

c:\>perl -d test.pl

Loading DB routines from perl5db.pl version 1.19
Editor support available.

Enter h or `h h' for help, or `perldoc perldebug' for more help.

main::(test.pl:6):      my $ref = XMLin(<<XML
main::(test.pl:7):      <config>
main::(test.pl:8):          <wrapper name="testName 1.0.3" script="/us
+r/people/ltorvalds/apps/wrapper.pl" app="testApp.exe">
main::(test.pl:9):              <envVar name="TMPDIR" value="/usr/tmp"
+/>
main::(test.pl:10):             <envVar name="APPDIR" value="/usr/bin"
+/>
main::(test.pl:11):         </wrapper>
main::(test.pl:12):     </config>
main::(test.pl:13):     XML
main::(test.pl:14):     );
  DB<1> n
main::(test.pl:15):     my $wrapName = "testName 1.0.3";
  DB<1> x $ref
0  HASH(0x1cb36d0)
   'wrapper' => HASH(0x1cc3a10)
      'app' => 'testApp.exe'
      'envVar' => HASH(0x1cf4b20)
         'APPDIR' => HASH(0x1cf4be0)
            'value' => '/usr/bin'
         'TMPDIR' => HASH(0x1ce6d34)
            'value' => '/usr/tmp'
      'name' => 'testName 1.0.3'
      'script' => '/usr/people/ltorvalds/apps/wrapper.pl'
  DB<2>
[download]

No arrays there, just hashes.