Hi trainwrecktwostep,
This is a very odd issue, as there should be no difference in what you hear in the DAW, once it is converted to digital.
Can you please provide some specifics on the computer you have? Mac/PC, OS version?
Which Scarlett do you have?
You are also welcome to contact us directly for support:
http://us.focusrite.com/answerbase/contact
Best regards.