Was the problem autovivification in sub getSignalsWithValsInTimeWindow() ?

if(exists $lastKnownSigValHRef->{$vcdFile}) {
  foreach my $signalId (keys %{$lastKnownSigValHRef->{$vcdFile}}) {
   foreach my $signalNm (keys %{$lastKnownSigValHRef->{$vcdFile}->{$signalId}}) {

  #### this line is creating the extra signals 
  #### as you check the lowest level
    if(!exists $inTimeRangeSignalsH{$vcdFile}{$signalNm}{$signalId}) {


     $sigsNotInTimeRangeH{$vcdFile}{$signalNm}{$signalId} = $lastKnownSigValHRef->{$vcdFile}->{$signalId}->{$signalNm}->{$hierScope}->[0];
    } 
   }
  }
 }