I have a banner with a link defined as "navto://collection/september_october_2016/article/so16_oow_preview". The banner is used on the "september_october_2016" collection browse page. In this context, the link sends the user to the first article in the collection, not the article named in the link.
If I put this same link on a banner in a different collection's browse page, it works fine. In other words, it appears that the "navto://collection/[collection_name]/article/[article_name]" format doesn't work if you are trying to point to create a link on a banner that points to the same collection that contains the banner.
This problem only occurs in iOS preflight apps, not Android preflight apps. I tested with version 2016.11 in both cases.
A "navto://article/so16_oow_preview" link works fine, but then I don't get the ability to swipe left or right to adjacent articles in the collection.
As I mentioned in my first post, this is happening is custom preflight app builds, built with version 2016.11.
The problem exists on iPads and iPhones, but not Android devices.
I can verify that I'm using the article name and not the article title. I've tried this with several different articles, just in case there was some obscure problem with the article name, or it was being miss-typed or something.
In your tests, did you put the banner on the browse page of the collection that you are linking to in the banner? That is where the problem seems to lie.