Hi,

 1) All my contents go in one chapter, everything from all the toctrees 
> ends up as Chapter 1 for some reason. 
>

Please check your index.rst. Is there "Contents" heading before toctree 
definition?
If true, Sphinx recognized the heading is a top level chapter.
 

>  2) Even though I have set maxdepth to 3 in the main toc, I only see one 
> level of headers in the table of contents
>

Hmm... it's strange. But I updated the mechanism at 1.4 series.
So I want to upgrade your Sphinx to newest and try it again.
 

>  3) Documents in the hidden toctrees are listed in the table of contents. 
> For example, I have a set of copyright statements and such in a hidden 
> toctree to prevent warnings when I build, and it shows up in the PDF 
> document table of contents


"hidden" option does not mean "not listed in the ToC".
"hidden" option is described as following:

This will still notify Sphinx of the document hierarchy, but not insert 
> links into the document at the location of the directive – this makes sense 
> if you intend to insert these links yourself, in a different style, or in 
> the HTML sidebar.

http://www.sphinx-doc.org/en/stable/markup/toctree.html

It does not generate toctree links at the location only.

If you want to prevent warnings, please mark the document as :orphan:.
To use it, please refere following page:
http://www.sphinx-doc.org/en/stable/markup/misc.html?highlight=orphan#file-wide-metadata

Thanks,
Takeshi KOMIYA

2016年9月13日火曜日 6時57分46秒 UTC+9 EMK:
>
> I've been focusing on HTML for several months and now I'm trying to build 
> PDF (via latexpdf) from the same files. 
>
> I have one main toctree and several hidden toctrees. 
>
> I'm having these problems:
>  1) All my contents go in one chapter, everything from all the toctrees 
> ends up as Chapter 1 for some reason. 
>  2) Even though I have set maxdepth to 3 in the main toc, I only see one 
> level of headers in the table of contents
>  3) Documents in the hidden toctrees are listed in the table of contents. 
> For example, I have a set of copyright statements and such in a hidden 
> toctree to prevent warnings when I build, and it shows up in the PDF 
> document table of contents
>
> Note: We haven't updated from Sphinx 1.3 yet, so if that makes a 
> difference we can upgrade. 
>
> Here's an example of how my index.rst file looks: 
>
> .. toctree::
>    :maxdepth: 3
>    :name: main
>    
>    intro
>    common_tasks
>    settings
>    support
>    
>    :ref:`genindex`
>    :ref:`search`
>    
>    appendix_1
>    appendix_2
>
> .. toctree::
>    :hidden:
>    :maxdepth: 1
>    :name: common_tasks_toc
>    
>    task_1_overview
>    task_2_overview 
>
> .. toctree::
>    :hidden:
>    :maxdepth: 1
>    :name: settings_toc
>  
>    settings_topic_1
>    settings_topic_2
>    settings_topic_3
>
> .. toctree::
>    :hidden:
>    :name: hidden files
>    
>    frontmatter
>    doc_warnings
>    license_info
>
> Here is what I am getting in my PDF table of contents: 
>
> CONTENTS 
>
> 1. Contents 
>
>  1.1    About MyProduct
>  1.2    Common Tasks for MyProduct
>  1.3    MyProduct Settings
>  1.4    Contacting Support
>  1.5    Appendix 1: Something Not Very Important
>  1.6    Appendix 2: Something Else Of Limited Interest
>  1.7    Task 1 Overview
>  1.8    Task 2 Overview
>  1.9    How To Set Item1
>  1.10  How To Set Item2
>  1.11  How To Set Item3
>  1.12  Index and Search
>  1.13  Copyright Information 
>  1.14  Warnings Used in This Document
>  1.15  License Information
>
> What am I doing wrong here? 
>

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