UNO Timer 1 CTC mode not resetting TCNT1
It sounds as though timer 1 has not in fact been set to wavegen mode 4. You can ensure that it is by also clearing the other bits of WGM1:

TCCR1A &amp;= ~(_BV(WGM10) | _BV(WGM11));
TCCR1B &amp;= ~_BV(WGM13);