kafka streams not fetching all records - apache-kafka

Question

I have a java Kafka streams application that reads from a topic do some filtering and transformations and writing the data back to Kafka to a different topic.
I print the stream object on every step.
I noticed that if I send more than dozens of records to the input topic, some records are not consumed by my Kafka streams application.
when using kafka-console-consumer.sh to consume from the input topic, I do receive all records.
I'm running Kafka 1.0.0 with one broker and one partition topic.
Any idea why?
public static void main(String[] args) {
final String bootstrapServers = System.getenv("KAFKA");
final String inputTopic = System.getenv("INPUT_TOPIC");
final String outputTopic = System.getenv("OUTPUT_TOPIC");
final String gatewayTopic = System.getenv("GATEWAY_TOPIC");
final Properties streamsConfiguration = new Properties();
streamsConfiguration.put(StreamsConfig.APPLICATION_ID_CONFIG, "PreProcess");
streamsConfiguration.put(StreamsConfig.CLIENT_ID_CONFIG, "PreProcess-client");
streamsConfiguration.put(StreamsConfig.BOOTSTRAP_SERVERS_CONFIG, bootstrapServers);
streamsConfiguration.put(StreamsConfig.DEFAULT_KEY_SERDE_CLASS_CONFIG, Serdes.String().getClass().getName());
streamsConfiguration.put(StreamsConfig.DEFAULT_VALUE_SERDE_CLASS_CONFIG, Serdes.String().getClass().getName());
streamsConfiguration.put(ConsumerConfig.AUTO_OFFSET_RESET_CONFIG, "earliest");
streamsConfiguration.put(StreamsConfig.COMMIT_INTERVAL_MS_CONFIG, 300L);
final StreamsBuilder builder = new StreamsBuilder();
final KStream<String, String> textLines = builder.stream(inputTopic);
textLines.print();
StreamsTransformation streamsTransformation = new StreamsTransformation(builder);
KTable<String,Gateway> gatewayKTable = builder.table(gatewayTopic, Consumed.with(Serdes.String(), SerdesUtils.getGatewaySerde()));
KStream<String, Message> gatewayIdMessageKStream = streamsTransformation.getStringMessageKStream(textLines,gatewayKTable);
gatewayIdMessageKStream.print();
KStream<String, FlatSensor> keyFlatSensorKStream = streamsTransformation.transformToKeyFlatSensorKStream(gatewayIdMessageKStream);
keyFlatSensorKStream.to(outputTopic, Produced.with(Serdes.String(), SerdesUtils.getFlatSensorSerde()));
keyFlatSensorKStream.print();
KafkaStreams streams = new KafkaStreams(builder.build(), streamsConfiguration);
streams.cleanUp();
streams.start();
// Add shutdown hook to respond to SIGTERM and gracefully close Kafka Streams
Runtime.getRuntime().addShutdownHook(new Thread(() -> {
streams.close();
}));
}