You could put all the values in array references indexed by your two-level hash. Something like this:

foreach $f (@files) {
  open FILE, $f or die "Error: $!";
  while(<FILE>) {
    chomp;
    my ($k,$v)=split("=",$_,2);
    # Assume dn= comes before other lines
    $level1=$k, next if $k eq "dn";
    unless ($level1) {
      die "Need to get dn= line first\n";
    }
    push @{$hash{$level1}{$k}}, $v;
  }
  close FILE;
}
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Then you will have something like this:

  $hash{machinename}{config}=["2000"]
  $hash{machinename}{speed}=["19200"]
  $hash{machinename}{setting}=["value1", "value2", "value3"]
  $hash{machinename2}{config}=["2020"]
  etc.
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And then do comparisons or anything else you need. See chapter 4 of The Perl Cookbook for examples of how to do fancy array operations, including comparisons.