tedster - 3:16 pm on May 20, 2011 (gmt 0)
You're right that a canonical link element was not going to fix that situation. As long as those 301 redirects are in place, then you are probably getting old information in the report.
Can you see in your own server logs if googlebot is still requesting those incorrect page URLs in present time, and if your server always responding with the 301? If that is the case, then you can just ignore the messages.