Hi Bob
 
I may be leading you up the garden path but.....
 
Where you plug the mini jack in is where you would normally plug in your el cheapo set of computer speakers in if you didn't have your nice interface and wasn't interested in recording....  correct? Instead you route that output through your interface rather than through a set of speakers.
 
So my initial post I suspect may still apply to your internal sound chip even though you are doing what you are doing otherwise Windows may remove frequencies that would instead go to a woofer... have you tried doing it yet to see what I mean?
 
Thanks
 
Alex

For just this reason, I put a patch panel (mostly set to half-normal) and a 1U rack mixer (Behringer) in my rack. I do the prudent thing of only using my Focusrite for recording/editing/mixing on my wall-hung monitors and the on-board sound for all else. This way I can route the Windows sound to my monitors easily, but also patch anything directly into/through my Saffire system, so I can easily transcribe and patch in sound sources. I can even simply and directly record from internet radio, or my house music system to capture loop material (I use Sonos for sound management). For $150 investment, it has dramatically simplified my routing issues, and is very useful for additional headphone mixes and auditioning. I have one of the Saffire outputs into the mixer, and split the output into 2 stereo slices of the patch panel.