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Originally Posted by janvanmaar
This is a speculation but I guess that Marco is using Amazon/Mobipocket tools indeed - Instapaper was reported to work with the new layout a day after the very first 3.1 candidate was released - not impossible but rather unlikely that he would have noticed and reverse-engineered the issue within a day.
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I doubt that Amazon actually changed their format for the 3.1 release--rather, they are probably exploiting a proprietary "feature" of their format that has always been there but not created any issues until they introduced the "Sections & Articles" view.
Note that if you select "Articles List" from the "Sections & Articles" view you get the linear list of articles as was available prior to 3.1, and the BACK button works properly if you select an article from this list and the press BACK. Interestingly, how you scroll to the "Article List" affects whether it works properly. If you scroll down the left side of the "Sections & Articles" page (through the section list) it works properly. However, if you scroll down the right side (via the article list) you get a wierd view of the article list (one per screen with the article title at the top, and the select button takes you back to the "Sections & Articles" view instead of the article).
I'm guessing the Kindle isn't doing page navigation for periodicals in a pure browser-style fashion (if it was, these problems wouldn't occur). Rather, I suspect the Kindle is building a linked structure representing the periodical contents and some of those links end up missing (in the case of going BACK to the "Sections & Articles" view from an article, so section 1 article 1 is the default) or they are pointing somewhere that doesn't make sense (in the case of scrolling the "Articles List" via the right side of the "Sections & Articles" view). Prior to 3.1, this structure was simpler. Now, it is more complex and there is something critical in the Kindle format that Calibre is missing, hence the problems.