ATMega328p (Arduino) Timer1 set-up
The Arduino core library configures the Timer 1 for phase-correct PWM at
about 490&nbsp;Hz. Then you are setting some configuration bits in the
timer's control registers without clearing the bits that had previously
been set by the Arduino core. If you want to use the timer for your own
purposes, and configure it by yourself, you should completely overwrite
the core's configuration with your own. For that, use the = operator
rather than |=, as in:

OCR1A  = 99;                         //Count to 400us
TIMSK1 = (1 &lt;&lt; OCIE1A);              //Enable interrupt
TCCR1A = 0;
TCCR1B = (1 &lt;&lt; WGM12)                //Mode 4, CTC
       | (1 &lt;&lt; CS11) | (1 &lt;&lt; CS10);  //Prescaler 64