I'm having the same problem. Canonical link is duplicating the alias for me.

I read other posts about avoiding duplicate menu items or sub categories but I don't have any of that. I just have one menu item called blog that points to one category and still articles in that category have canonical links with duplicate aliases. Also tried upgrading to the latest and using the advanced sef parameter to on. That didn't help.

Anyone have any ideas on how to fix without buying a separate plugin to mask the problem.