From your description, it sounds like you have a very low signal level coming into your computer, and are then compensating by turning up the output very high. This would cause a problem triggering the noise gate, and possibly you are hearing the noise gate at the 'floor' level until it triggers, then you hear a very loud signal.
Make sure you have a reasonable level coming into your audio interface and into S-Gear. At least into the yellow when you hit a chord hard. You should then find that the noise gate works well with the factory presets.