VGA library for Arduino UNO and ATMega328

Using Arduino Displays
12

Here, in particular:

  while(1) { // this is the main loop
    if (timer == 2) {
      // timed code here....
      shiftFwd(&H_GREEN_data[0]);
      shiftFwd(&H_BLUE_data[0]);
      timer=0;
    }

You are waiting for the ISR to fire anyway, and when it does you will have a few clocks before you notice if timer == 2. So add a sleep:

  while(1) { // this is the main loop
    sleep_mode ();   // wake in a predictable way
    if (timer == 2) {
      // timed code here....
      shiftFwd(&H_GREEN_data[0]);
      shiftFwd(&H_BLUE_data[0]);
      timer=0;
    }

In initialization, make sure sleep mode is idle:

  set_sleep_mode (SLEEP_MODE_IDLE);