If you are using Volume Leveling, this will reduce the average playback volume to -23dB.
This is intentional, as you need that much headroom to prevent either clipping during playback, or unevenness in the leveling.
If you are using an exclusive output (e.g. WASAPI) what you should be able to do is, with playback stopped, go into the Windows sound control panel and reduce the volume level for your output device to 54%. (which I believe corresponds to -23dB)
This should help minimize the difference between the system sounds and Media Center's playback, as long as you use the amplifier to control the volume rather than using the Internal volume control.
You may find that 54% is too much though, as that would be the maximum level for system sounds, rather than the average level. You might find that something in the 54-74% range is better.
You could continue to use the Internal volume control, but be aware that as you reduce the volume in Media Center, it will make the system sounds louder relative to the music level.