Arduino 1.6.3 not working for older sketches

I was updating my Arduino software from 1.0.6 to 1.6.3 and I had troubles with using older sketches. I use an Arduino UNO SMD version. There is no error thrown the code is just hanging using the monitor. I’m using a code from Manila Taft to set the time and date on a RTC DS 1307. The code is uploading fine but will hang in the monitor when the year is entered. I do not know what to do nor how to debugging since no error message is giving some indicators. Any ideas or same issues faced? Thank you very much.

///////////////////////////////////////////
// RTC data and time setter              //
//                                       //
// This sample program allows the user   //
// to set the date and time of an RTC    //
// using I2C.                            //
//                                       //
// Codes by:                             //
// eGizmo Mechatronix Central            //
// Taft, Manila, Philippines             //
// http://www.egizmo.com                 //
// April 15, 2013                        //
///////////////////////////////////////////

#include <Wire.h>
const int DS1307 = 0x68; // Address of DS1307 see data sheets
const char* days[] =
{"Sunday", "Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday"};
const char* months[] =
{"January", "February", "March", "April", "May", "June", "July", "August","September", "October", "November", "December"};

// Initializes all values: 
byte second = 0;
byte minute = 0;
byte hour = 0;
byte weekday = 0;
byte monthday = 0;
byte month = 0;
byte year = 0;

void setup() {
  Wire.begin();
  Serial.begin(9600);
  delay(2000); // This delay allows the MCU to read the current date and time.

  Serial.print("The current date and time is: ");
  printTime();
  Serial.println("Please change to newline ending the settings on the lower right of the Serial Monitor");
  Serial.println("Would you like to set the date and time now? Y/N");

  while (!Serial.available()) delay(10);
  if (Serial.read() == 'y' || Serial.read() == 'Y')

  // This set of functions allows the user to change the date and time
  {
    Serial.read();
    setTime();
    Serial.print("The current date and time is now: ");
    printTime();
  }


  Serial.println("Thank you.");
}

// Continuous function for converting bytes to decimals and vice versa
void loop() {
}
byte decToBcd(byte val) {
  return ((val/10*16) + (val%10));
}
byte bcdToDec(byte val) {
  return ((val/16*10) + (val%16));
}


// This set of codes is allows input of data
void setTime() {
  Serial.print("Please enter the current year, 00-99. - ");
  year = readByte();
  Serial.println(year);
  Serial.print("Please enter the current month, 1-12. - ");
  month = readByte();
  Serial.println(months[month-1]);
  Serial.print("Please enter the current day of the month, 1-31. - ");
  monthday = readByte();
  Serial.println(monthday);
  Serial.println("Please enter the current day of the week, 1-7.");
  Serial.print("1 Sun | 2 Mon | 3 Tues | 4 Weds | 5 Thu | 6 Fri | 7 Sat - ");
  weekday = readByte();
  Serial.println(days[weekday-1]);
  Serial.print("Please enter the current hour in 24hr format, 0-23. - ");
  hour = readByte();
  Serial.println(hour);
  Serial.print("Please enter the current minute, 0-59. - ");
  minute = readByte();
  Serial.println(minute);
  second = 0;
  Serial.println("The data has been entered.");

  // The following codes transmits the data to the RTC
  Wire.beginTransmission(DS1307);
  Wire.write(byte(0));
  Wire.write(decToBcd(second));
  Wire.write(decToBcd(minute));
  Wire.write(decToBcd(hour));
  Wire.write(decToBcd(weekday));
  Wire.write(decToBcd(monthday));
  Wire.write(decToBcd(month));
  Wire.write(decToBcd(year));
  Wire.write(byte(0));
  Wire.endTransmission();
  // Ends transmission of data
}


byte readByte() {
  while (!Serial.available()) delay(10);
  byte reading = 0;
  byte incomingByte = Serial.read();
  while (incomingByte != '\n') {
    if (incomingByte >= '0' && incomingByte <= '9')
      reading = reading * 10 + (incomingByte - '0');
    else;
    incomingByte = Serial.read();
  }
  Serial.flush();
  return reading;
}

void printTime() {
  char buffer[3];
  const char* AMPM = 0;
  readTime();
  Serial.print(days[weekday-1]);
  Serial.print(" ");
  Serial.print(months[month-1]);
  Serial.print(" ");
  Serial.print(monthday);
  Serial.print(", 20");
  Serial.print(year);
  Serial.print(" ");
  if (hour > 12) {
    hour -= 12;
    AMPM = " PM";
  }
  else AMPM = " AM";
  Serial.print(hour);
  Serial.print(":");
  sprintf(buffer, "%02d", minute);
  Serial.print(buffer);
  Serial.println(AMPM);
}


void readTime() {
  Wire.beginTransmission(DS1307);
  Wire.write(byte(0));
  Wire.endTransmission();
  Wire.requestFrom(DS1307, 7);
  second = bcdToDec(Wire.read());
  minute = bcdToDec(Wire.read());
  hour = bcdToDec(Wire.read());
  weekday = bcdToDec(Wire.read());
  monthday = bcdToDec(Wire.read());
  month = bcdToDec(Wire.read());
  year = bcdToDec(Wire.read());
}

Some things I noticed:

while (!Serial.available()) delay(10);
  if (Serial.read() == 'y' || Serial.read() == 'Y')

You are doing a read, then compare with ‘y’, then do another read. So you are reading two characters but you expect the user to only enter one character

if (incomingByte >= '0' && incomingByte <= '9')
      reading = reading * 10 + (incomingByte - '0');
    else;
    incomingByte = Serial.read();

What does the ‘else’ do?

Why do you call Serial.flush in readByte? flush only affects the output buffer

Hello olf2012,

thank you very much for the findings. I'll check that out.