Solar Charge Controller: Voltage increase problem
I have resolved the issue by reading the arduino voltage. Arduino has this great feature where you can read the current voltage. If anyone is facing the similar issue use the below code to read the voltage:

long readVcc() 
{
  long result;
  // Read 1.1V reference against AVcc
  ADMUX = _BV(REFS0) | _BV(MUX3) | _BV(MUX2) | _BV(MUX1);
  delay(2); // Wait for Vref to settle
  ADCSRA |= _BV(ADSC); // Convert
  while (bit_is_set(ADCSRA,ADSC));
  result = ADCL;
  result |= ADCH&lt;&lt;8;
  result = 1125300L / result; // Back-calculate AVcc in mV
  return result;
}


Above code will return the voltage of the arduino.