Hi,
Please make a fix that prevents link rel=canonical insertion into the valid pages that don't need redirection. those links should be used only in pages you wish to redirect.
until then, people should *disable canonical* option if they don't want to see their pages disappearing from Google.
thanks!
ps. http://www.google.com/support/webmasters/bin/answer.py?hl=en&answer=139394
http://seolutions.net/blog/google-canonical-url-problems-and-link-disappearance-from-serp-s/