From some discussion on a canning group to which I subscribe, I think the issue with canning it stops the fermentation process - ending the "probiotic" properties of the kraut. I've never tried it, either way... but here's "safe" guidelines from the National Center for Home Food Preservation for both fermenation and canning.
http://www.uga.edu/nchfp/how/can_06/sauerkraut.html