I've been looking into this and have found:
1) Instapaper files (sent from Instapaper) have a single section with the captured pages appearing as articles within that section. The BACK button does indeed return from an article to the corresponding cursor position on the Sections & Articles view.
2) If I convert the Instapaper MOBI file to HTML using ebook-convert I find the generated toc.ncx file to be devoid of any table of contents info. Specifically, this is all I got for an Instapaper file with 6 articles:
<?xml version='1.0' encoding='utf-8'?>
<ncx xmlns="http://www.daisy.org/z3986/2005/ncx/" version="2005-1" xml:lang="en">
<meta content="6f4b85b8-9278-43e2-a6aa-a995e0ed3953" name="dtb:uid"/>
<meta content="1" name="dtb:depth"/>
<meta content="calibre (0.7.45)" name="dtb:generator"/>
<meta content="0" name="dtb:totalPageCount"/>
<meta content="0" name="dtb:maxPageNumber"/>
I also noted that the HTML file uses H1 tages for the article titles, and I'm surmising that the Kindle is auto-generating the table of contents from the H1 tags. If I open the Instapaper MOBI file in Calibre or Mobipocket reader there is no table of contents.
I've looked at the output from Calibre, using ebook-convert to take it from MOBI to HTML. What I've found is Calibre doesn't use H1 to identify article titles--it generates a complete toc.ncx file which references articles using ID labels.
There is a strange error in the ebook conversion from MOBI to HTML for files with more than one feed (i.e. section). The references to section TOC's in toc.ncx end up looking like
<navPoint class="chapter" id="ff83e450-3d2b-42e9-a233-9a8f90f9fd82" playOrder="0">
Note the missing "f" in ="Daily_Caller.html#eed_0/index.html" it should be ="Daily_Caller.html#feed_0/index.html." During the conversion, ebook-convert spat out a bunch of file not found messages, as in
C:\Users\Nick\Calibre Library>ebook-convert daily.mobi dailydir1
1% Converting input to HTML...
InputFormatPlugin: MOBI Input running
on C:\Users\Nick\Calibre Library\daily.mobi
Parsing all content...
Forcing Daily_Caller.html into XHTML namespace
Referenced file 'feed_6/index.html' not found
Referenced file 'feed_2/index.html' not found
Referenced file 'feed_4/index.html' not found
Referenced file 'feed_3/index.html' not found
Referenced file 'feed_5/index.html' not found
Referenced file 'feed_0/index.html' not found
Referenced file '%20http%3a//twitter.com/Chris_Moody%20' not found
Referenced file 'feed_1/index.html' not found
Referenced file 'feed_10/index.html' not found
Referenced file 'feed_9/index.html' not found
Referenced file 'feed_8/index.html' not found
Referenced file '../2011/02/10/trump-at-cpac-points-to-white-house-run/' not found
34% Running transforms on ebook...
Merging user specified metadata...
Flattening CSS and remapping font sizes...
Source base font size is 12.00000pt
Cleaning up manifest...
Trimming unused files from manifest...
Trimming 'images/00002.jpg' from manifest
Trimming 'images/00001.jpg' from manifest
Trimming 'images/00003.jpg' from manifest
Creating OEB Output...
67% Creating OEB Output
OEB output written to C:\Users\Nick\Calibre Library\dailydir1
Output saved to C:\Users\Nick\Calibre Library\dailydir1
I'm not sure if this is representative of a fault in the MOBI file or in ebook-convert to HTML.
Any suggestions from MOBI experts would be appreciated. There is definately something wrong somewhere, and perhaps it is in Calibre after all, if only a mismatch between how the Kindle handles MOBI periodical files and how Calibre structures them.