Like DJX says, until you get Windows and Jaws to not use the Motu and Sonar to use the Motu exclusively, you're going to have issues.
Regarding note taking, why are you using a second computer for this? Why not just open up Notepad on the DAW, and ALT+TAB to it when you want to make a note of something? Are you writing a novel while simultaneously recording music?
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