I had this problem for the longest and I found what seems to have been a damn good solution. When I was recording in Cool Edit, my vocals would get progressively more and more offbeat the longer the track went on. I couldn't find an answer until I searched the Adobe site.

What you need to do is go into the "Settings" and click on the Multitrack tab. In there, simply check the box that says "Correct For Drift In Recordings" and voila!

Just dropping this in case anyone experiences the same problem.

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Soundclick