Does anything in your app set $/?

Try adding the local line below:

sub returnVersion()
{
   my $cmdToExecute = "dds_cmd -Version ";
   my $versionNum;
   my $PH;
   if (!open($PH, "$cmdToExecute 2>&1 |")) {
      print STDERR "Failed to execute command:($cmdToExecute)--$!\n";
      exit 1;
   }

   local $/ = "\n"; ###################

   while (my $line = <$PH>) {
      if (index($line, "Command Execution ") != -1){
         $line =~ s/^.+version\s|\.0.$//g;
         $versionNum = $line;
      }
   }
   close($PH);
   return $versionNum;
}
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