Making a composite waveform using a single TIMER interrupt
Woo, solved it.  My ISR code was completely wrong.  Works using:

ISR(TIMER2_COMPA_vect)
{
  if (timer2_signal_toggle_count != 0)
  {
    // toggle the pin
    if(signal_state == 1)
        *timer2_pin_port ^= timer2_pin_mask;

    if (timer2_toggle_count &gt; 0)
      timer2_toggle_count--; 
    else
    {
        TIMSK2 &amp;= ~(1 &lt;&lt; OCIE2A);                 // disable the interrupt
        *timer2_pin_port &amp;= ~(timer2_pin_mask);   // keep pin low after stop
    }
     timer2_signal_toggle_count --; 
  }
  else
  {
    timer2_signal_toggle_count = signal_cycle_count;
    timer2_toggle_count --;
    if(signal_state == 1)
    {
        signal_state = 0;
        *timer2_pin_port &amp;= ~(timer2_pin_mask);
        //*timer2_pin_port ^= timer2_pin_mask;
    }
    else 
    {
        signal_state = 1;
        *timer2_pin_port ^= timer2_pin_mask;
    }
  }
}


I was trying to just AND the signal state into the original pin state, which was completely the wrong thing to do.