So over the months I've owned it, I've come to learn that the Pro-3 is a temperamental beast when it comes to volume. If you have all 3 oscillators running full tilt into the filter, chances are that you're going to overdrive the filter. This may result in the sound breaking up some, and thus making the synth kind of "bottom out" and lose bass response.
Try rolling back the volume of the oscillators some to see if that helps. You may have to compensate for the lost volume with either the master volume or the preamp on your audio interface, mixer or whatever. Furthermore, when designing future patches you'll want to keep headroom in mind so you have space to get louder when needed.