Yep. Unlike more sophisticated PWM converters, where the pulses come at a fixed frequency and varying duty cycle (strength), the MC34063 works generating a fixed pulse train, then selectively omitting pulses from it when the output voltage is high enough. This means that if one single pulse of the fixed duration is too much, you still get the whole thing whether you like it or not. You can try decreasing CT to shorten the pulses (this will affect your maximum output current though), adding a small dummy load, using a different (PWM) chip, or just dealing with it.
MC34063's applications are usually limited to non-variable cases, where the load will look pretty much exactly like the load you designed it for at all times.