I had another thought too. Just because the pages say they are indexed in Google WMT, doesn't mean the new content including the new canonical tags have been crawled or added to the index yet.
I recently did a similar project adding canonical tags to an ecommerce site. The new URLs are only showing up correctly in the search results maybe 10% of the time, even for pages I know have been crawled and I submitted a week ago. The important thing is that more URLs are updated each day.
I dont believe they throw out their index the first time they crawl an established page and something has changed. I believe the index gets changed as they continue to crawl they compare versions and index data based on multiple crawl agregates, especially if it is for existing pages that have been in the index for a while. So in other words, if they compare 20 recent crawls and only see 1 version as being different, they may not throw out the old version right away until they crawl it multiple times and see that the the new version exists, say 5 or 10 of the most recent 20 crawls. BTW I don't have any data to back that up just my personal observation/theory.