This problem has been driving me nuts forever, and I finally found a solution courtesy of
http://www.thesession.org/discussions/display/15082. I'll paste what I found here for good measure:
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The problem you are experiencing is that Audition is releasing the ASIO driver when it is no longer the window in focus (the selected application window). What you need to do is to tell Audition not to release the ASIO driver when you change the window that is in focus.
On the menu do the following
Edit/Audio Hardware Setup (Third from the bottom)
-> [ ] Release ASIO Driver in Background
This is located toward the middle of the dialog box vertically.
Un-Check the check-box so that Audition will stay connected to the ASIO driver even when the window is "out of focus".
Thanks to Dan Proctor
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