No need to loop through the hash keys to find a match

foreach my $okey (keys %identifier) {
   foreach my $skey (keys %{$identifier{$okey}}) {
     if (exists $identifier{$okey}) {

Try

#!/tools/perl/5.8.8/linux/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $report ="/ice_pnr/pnr19/nadder/lzhong/uibnd4h/lzhong.i14socnd.uibn
+d4h.44/uibnd4h/r2g2/blocks/INTEL14.P1273.6/uibnd4h_bot_sta/40_finish/
+tmp/trans10/max_trans_summary.list";
my $waiver = "/home/leeyong1/waiver.csv";
my $result = "/home/leeyong1/output.file";
print "script -report ($report) -waiver ($waiver) -output ($result)\n"
+;

# Read the violations file into the hash
#klmn124,100.00,2500.00,"justifiedbyChan","Date:14/4"
my %identifier = ();
open my $filter, '<', $waiver or die "$!";
while (my $vline = <$filter>) { 
  next unless $vline =~ /\S/; # skip blank lines  
  my ($pin, $t1, $t2, @note) = split /,/, $vline;
  $identifier{$pin}{'t1'} = $t1;
  $identifier{$pin}{'t2'} = $t2;
}
print Dumper \%identifier;

#Read input file line by line
open my $input, '<', $report or die "$!";
open my $output, '>', $result or die "$!";
#abcd123 klmn123 100.00 1000.00 -900.00 (VIOLATED)
while (my $wline = <$input>){
  my ($scenario, $pin, $t1, $t2, $diff, $status) = split /\s+/, $wline
+;
  # overwrite values if match
  if (exists $identifier{$pin}) {
    $t1 = $identifier{$pin}{'t1'};
    $t2 = $identifier{$pin}{'t2'};
    $diff = sprintf "%.2f",$t1-$t2; 
    $status = '(WAIVED)';
  }
  print $output "$scenario $pin $t1 $t2 $diff $status\n";
}
close $filter;
close $input;
close $output;
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poj