i have tried ur links and put some debug but it seem the second if doesnt encounter. only n times display of "into the second loop .." please fine the full code

#! C:/perl/bin/perl.exe

use strict;
use warnings;
use File::Copy;
use File::Basename;
use Cwd;
use Data::Dumper;
use File::Copy::Recursive qw(dircopy) ;

my $fullpath = cwd();
my $value = 0;
my $file = basename($fullpath);
my $dir = dirname($fullpath);
print("$fullpath, $file, $dir");

opendir(my $pathindex, $dir ) or die "Couldn't read index : $!\n";
while (my $currentfile = readdir($pathindex)) {
         print "\nCurrent Directory File $value\t";
         print "$currentfile","\n";
     $value++;
}

print "\nENTER THE PROJECT NAME FROM ABOVE LIST\n";
my $projectdir = <STDIN>;
chop($projectdir);
my $projectdirpath = "/"."$projectdir";
my $workingdirectory = ($dir.$projectdirpath);
chdir($workingdirectory."/trunk"); 
my $newpath = cwd();

my $source_dirrtl;
my $target_dirrtl ;            # = ("$newpath"."/rtl2");
opendir(my $index, $newpath ) or die "Couldn't read index : $!\n";
while (my $file = readdir($index)) {
       if ($file eq "rtl" ) {
         if(chdir($newpath."/rtl")) {
          my $currentworkingdir = cwd();
          $source_dirrtl = $currentworkingdir;
          $target_dirrtl = ("$newpath"."/rtl2"); 
      }
         last;
     }     

     elsif ($file eq "vhdl") {
         if(chdir($newpath."/vhdl")) {
          my $currentworkingdir = cwd();
          $source_dirrtl =   $currentworkingdir;
          $target_dirrtl = ("$newpath"."/vhdl2"); 
      }
         last;
     }
}
closedir($index);
my $configdirc = $newpath."/configdir";
chdir($configdirc);
opendir( my $indexconfig,$configdirc ) or die "Couldn't enter config d
+irectory: $!\n";
          print("\nCONFIGURATION FILES IN THE CONFIG DIRECTORY \n");
          my @rtlfilelist = glob "*.icfg";
          print ("\n@rtlfilelist \n");

closedir($indexconfig);

my $cChipId;
my $cSubVersId;
my %data_ids;
my $readline;
my $toplevelentity;
my $ivariant_name;
print "\nENTER THE CONFIGURATION FILE NAME FROM THE ABOVE LIST \n";
my $configfile = <STDIN>;
open (my $CFILE,$configfile ) || die "couldnt open file: $!";  
   while ($readline = <$CFILE>) {
       chomp $readline;
       my ($key , $value) = (split /::/, $readline);
       $data_ids{$key} = $value if $key;
       next if $readline =~ /^ $/;
   }
   close($CFILE); 
   for my $key (keys %data_ids) {
       $cChipId = $data_ids{'chipid'};
       $cSubVersId = $data_ids{'subversid'};
       $toplevelentity = $data_ids{'Top_level_entity'};
       $ivariant_name = $data_ids{'Variant_Name'};
   }


my $source_dirsim = ("$newpath"."/sim");
my $target_dirsim1 = ("$newpath"."/sim2");


my $source_dirsynth;
my $target_dirsynth1 ;
opendir(my $indexs, $newpath ) or die "Couldn't read indexs : $!\n";
while (my $file = readdir($indexs)) {
       if ($file eq "par" ) {
         if(chdir($newpath."/par")) {
          my $currentworkingdir = cwd();
          $source_dirsynth = $currentworkingdir;
          $target_dirsynth1 = ("$newpath"."/par2"); 
      }
         last;
     }     

     elsif ($file eq "synth") {
         if(chdir($newpath."/synth")) {
          my $currentworkingdir = cwd();
          $source_dirsynth =   $currentworkingdir;
          $target_dirsynth1 = ("$newpath"."/synth2"); 
      }
         last;
     }
}
closedir($indexs);




mkdir($target_dirrtl,0777);
mkdir($target_dirsim1,0777);
mkdir($target_dirsynth1,0777);




my $filertl = dircopy($source_dirrtl, $target_dirrtl);
my $filesim = dircopy($source_dirsim, $target_dirsim1);
my $filesynth = dircopy($source_dirsynth, $target_dirsynth1);



opendir $source_dirsynth: $!";

chdir("$target_dirrtl");
my $m4file = "$projectdir".".m4";
open(MYFILE,">>$m4file"); 
  print MYFILE ("define(`m4_cChipId',`16#$cChipId#,16')\n");
  print MYFILE ("define(`m4_cSubVersId',`16#$cSubVersId#,16')\n");
  print MYFILE ("define(`m4_$projectdir',`1')\n");
  print MYFILE ("define(`m4_$ivariant_name',`1')\n");
  print MYFILE ("define(`m4_rtl',`rtl2')\n");
  if(my $output1 = `test.bat`){
        print("\n succesfully executed\n");    
 } 

chdir("$target_dirsynth1");
######################################################################
+##############################################
#added on 13/5/2016
opendir( my $synthdir,$target_dirsynth1) or die "Couldn't enter config
+ directory: $!\n";
          print("\nSYNTHESIS INPUT FILES IN CURRENT DIRECTORY \n");
          my $synthfilelist = glob "*.qsf";
          print ("\n$synthfilelist \n");

#closedir($target_dirsynth1);

       my $originalquartus ;
       my $latestquartus ;
       my $readlineqo;
       my $readlineql ;
#print "\nENTER THE CONFIGURATION FILE NAME FROM THE ABOVE LIST \n";
#my $configfile = <STDIN>;
open (my $OFILE,$synthfilelist) || die "couldnt open file: $!";  
   while ($readlineqo = <$OFILE>) {
       chomp $readlineqo;
       if ($readlineqo =~ /ORIGINAL_QUARTUS_VERSION/) { 
       my @originalqarray = (split / +/ , $readlineqo);
       $originalquartus = $originalqarray[3];
       print "\nthe original quartus $originalquartus\n";
         }
#next if $readlineqo =~ /^ $/;
#       }
#  close($OFILE); 

#open (my $LFILE,$synthfilelist) || die "couldnt open file: $!";  
#  while ($readlineql = <$LFILE>) {
#       chomp $readlineql;
       print "into the second loop $readlineqo\n";
       if ($readlineqo =~ /LAST_QUARTUS_VERSION/) {
       my @latestqarray = (split / +/ , $readlineqo);
       $latestquartus = $latestqarray[3];
       print "\nthe latest quartus $latestquartus\n";
       }
     next if $readlineqo =~ /^ $/;
    }       
   close($OFILE); 

closedir($target_dirsynth1);
######################################################################
+##############################################
print("\n Enter y or n to continue with synthesis \n");
my $choice = <STDIN>;
chop($choice);
if ($choice eq "y") {
  system ("qcmd.bat $toplevelentity");
}
else {
    print "continue manually with synthesis\n";
}
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block that is causing problem is inside #line with date of today. the whole code is running and even the last print statement also comes but after n times print of "into the second loop..".