Hi there!
Thanks for reaching out. My name is Erin, and I'm on the Moz Help Team.
Campaigns have a 90% tolerance for duplicate content. This includes all the source code on the page and not just the viewable text. So if a URL is at least 90% similar in code to another URL, this warning will appear. Although the pages in question are may appear to be different on the front end, they are actually duplicates based on this percentage (at least the example URLs I checked in your campaigns.)
You can run your own tests using this tool: http://www.webconfs.com/similar-page-checker.php
We don't know what standard Google uses, but it's safe to say they are a bit more sophisticated than us - so you might be okay in this regard as long as you have a couple hundred words of unique text per page. Google won't say how much duplicate content is too much, so we like to be better safe than sorry. 
Our crawler does recognize canonicals, so this might be happening because of where your canonicals tags are pointing. Pages are considered duplicates if their canonical tags point to different URLs. For example, DUPLICATE1 is considered a duplicate of DUPLICATE2 if the canonical tag for the first page is CANON1 while the canonical for the second URL is CANON2.
Since the canonical tags point to different pages it is assumed that CANON1 and CANON2 are likely to be duplicates themselves.
Here is how our system interprets duplicate content vs. rel canonical:
Assuming A, B, C, and D are all duplicates,
If A references B as the canonical, then they are not considered duplicates
If A and B both reference C as canonical, A and B are not considered duplicates of each other
If A references C as a canonical, A and B are considered duplicated
If A references C as canonical, B references D, then A and B are considered duplicates
For more information on using canonical tags, check out this great post by our very own Dr. Pete:
http://moz.com/blog/rel-confused-answers-to-your-rel-canonical-questions
Whew! That was a lot of information! If you still have questions, feel free to email us at help@moz.com with examples of any URLs you have questions about. 
Happy Tuesday!
Erin
We really want to help you troubleshoot this. Either follow up with in the support ticket we have open, or email us at 