The pulses look OK to me.
100-20=80 80/16=5 microseconds. at 0.5 milliseconds (500 microseconds) per division the pulse would be about 1/100th of a division.
10000-20 = 9980. 9980/16=623 microseconds or a little over 1 division.
I suspect the long delay before triggering is a wrap-around of the timer. Try resetting more of the registers:
#include <avr/io.h>
#include <avr/interrupt.h>
#define LEDPIN 13
void setup(){
pinMode(LEDPIN, OUTPUT);
cli(); // disable global interrupts
TCCR1A = 0; // Clear TCCR1A
TCCR1B = 0; // Clear TCCR1B
TCCR1C = 0; // Clear TCCR1C
TCNT1 = 0; // Clear the timer
TIMSK1 = 0; // Clear the interrupt mask
TIMSK1 |= (1 << OCIE1A); // enable timer compare interrupt channel A:
TIMSK1 |= (1 << OCIE1B); // enable timer compare interrupt channel B:
TCCR1A = B11110000; // Set OC1A/OC1B on Compare Match, clear OC1A/OC1B at BOTTOM
OCR1A = 20; // COMPA at 20/16ths microseconds
OCR1B = 40; // COMPB at 40/16th microseconds
sei(); // Enable global interrupts
attachInterrupt(0, start, RISING);
}
void loop(){
}
void start(){
//want to start/ restart the timer here
TCNT1 = 0; // Clear the timer
TCCR1B |= (1 << CS10); // prescaler=1 16 MHz clock
}
ISR(TIMER1_COMPA_vect){
digitalWrite(LEDPIN, HIGH);
}
ISR(TIMER1_COMPB_vect){
digitalWrite(LEDPIN, LOW);
TCCR1B = 0; //stop timer here
}