Stop timer set new value and start again AVR (Interrupt)
To stop the timer you have to clear the three bits CS10, CS11 and CS12. 

 TCCR1B |= (0 &lt;&lt; CS10);
 TCCR1B |= (0 &lt;&lt; CS12);


Those two lines has no effect on the register. Instead, use the following lines (Assuming CS11 stays cleared).

TCCR1B &amp;= ~(1 &lt;&lt; CS10);
TCCR1B &amp;= ~(1 &lt;&lt; CS12);