Beat Slicing?

I was watching course sample video on the Berklee site: http://lms-intro.www.berkleemusic.com/mod/resource/view.php?id=472243
where the instructor was going over a beat slicing example (you may need to be logged in to watch it). Initially I followed along with the workflow in Pro Tools then I wanted to see if I could translate it to X3 but I ran into a problem with audio quantization.
I bought a copy of the original song 'Amen Brother' by The Winstons to make sure I had the right starting point and noticed that I had to quantize the 4 measure sample before I could apply the workflow. That worked in PT, pretty much click and go, everything lined up nicely after quantization. However when I attempted to do the same thing in X3 I noticed that audio snap quantization didn't exactly line things up correctly. I think in the original recording there were some small delays between the right and left channels, if you zoom to the sample level you can see it. After quantization using audio snap the right and left channels were still not starting in the same place so it was not possible to slice on the grid.
It looks like audio snap might be averaging the two channels and applying the difference, is there a way to tell audio snap quantization to quantize both channels independently? Am I doing something wrong?