You'll find this more reliable

sub dequote {
   local *_ = \$_[0];
   s/^"(.*)"$/$1/;
   s/\\(.)/$1/g;
}


      if ($line =~ m/
        -([^\S"\\]+)           # An dashed identifier
        (?:                    # optionally followed by
          \s+                  # whitespace
          (                    # and either
            "(?:[^"\\]|\\.)*"  # a quoted string
            |                  # or
            [^\S"\\]+          # a bare identifer.
          )
        )?
      /x)
      {
         my ($opt, $arg) = ($1, $2);
         dequote($arg);
         $DATAFROMBATCHFILE[$counter]{$opt} = $arg;
      }
      elsif ($line =~ m/\bEND\b/)
      {
         $counter ++;
      }
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You're using a hash as an array again. Are you used to programming in PHP? I fixed it to use an array (meaning I changed {} to []. If the key to a hash is a number, chances are you should be using an array.