My code needs Serial.begin to work but I do not need Serial support in my code

The code now works... two things had to be done...

  1. The array was incorrectly dimensioned in the beginning of the code (embarrassing)... I also changed the way the array is used in the OCR1B ISR.
  2. In the OCR1A interrupt routine you needs to clear the interrupt. And to clear you need to write a 1 to the corresponding bit (so I write 255 to TIFR1) before you enable the interrupts again.

The now well working code

//Convenience macros
#define TC1_ConnectToPrescaler_8 TCCR1B &= ~((1<<CS12) | (1<<CS10)) ; TCCR1B |= (1<<CS11)
#define TC1_ClearOnCompareMatchWithOCR1A TCCR1A &= ~((1<<WGM11)|(1<<WGM10)); TCCR1B &= ~(1<<WGM13); TCCR1B |= (1<<WGM12)
#define TC1_EnableInterruptOnCompareMatchWithOCR1A TIMSK1 |= (1<<OCIE1A)
#define TC1_EnableInterruptOnCompareMatchWithOCR1B TIMSK1 |= (1<<OCIE1B)
#define TC1_DisableInterruptOnCompareMatchWith0CR1B TIMSK1 &= ~(1<<OCIE1B)

const byte PPM_Pin = 12;
volatile byte PPM_Progress = 0;
volatile word CHX_Pulse[8];

void setup () {
  pinMode(13,OUTPUT);
  pinMode(PPM_Pin, OUTPUT); 
  TC1_ConnectToPrescaler_8; //1 count = 0,5 µs
  TC1_ClearOnCompareMatchWithOCR1A;
  TC1_EnableInterruptOnCompareMatchWithOCR1A;
  OCR1A = 40000;
  for (byte i = 0 ; i < 8 ; i++){
    CHX_Pulse[i] = 800 + i*200;
  }
}

void loop () {
}

ISR(TIMER1_COMPA_vect){
  digitalWrite(PPM_Pin, LOW);
  PPM_Progress = 1;
  OCR1B = 800; 
  TIFR1 = 255;
  TC1_EnableInterruptOnCompareMatchWithOCR1B;
  digitalWrite(13,HIGH);
  digitalWrite(13,LOW); 
  return;
}

ISR(TIMER1_COMPB_vect){
  switch (PPM_Progress) {
    case 1: case 3: case 5: case 7: case 9: case 11: case 13: case 15: case 17:
      digitalWrite(PPM_Pin, HIGH);
      OCR1B = OCR1B + CHX_Pulse[((PPM_Progress + 1)/2) - 1]*2;
      break;
    case 2: case 4: case 6: case 8: case 10: case 12: case 14: case 16:
      digitalWrite(PPM_Pin,LOW);
      OCR1B = OCR1B + 800;
  }
  PPM_Progress++;
  if (PPM_Progress == 18) {
    TC1_DisableInterruptOnCompareMatchWith0CR1B;
  }
  return;
}