ATmega128 output compare normal mode. Generating a waveform with ISR
In Normal mode a timer does not reset when an output compare matches. Your first value in OCR3A should be the pulse width, and the second should be the pulse period. You will need to reset the timer by hand once the pulse period elapses. And read very carefully all the warnings in the datasheet about modifying OCR3A and TCNT3 while the timer is running.