cmendla - 8:30 pm on Apr 30, 2013 (gmt 0)
Just an update from my end. I installed a joomla extension that does SEF and also does canonical links. (Not sure if I can mention the name). The documentation is a bit fuzzy so I'm trying to figure out exactly how to make it work.
Supposedly their canonical link fix works well.
I also found a problem with another site where I have a separate menu for the mobile version. It looks like that is treated as a dupe. The simple fix there is to either get rid of the mobile menu or to use robots.txt to not count it.