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I'm writing my thesis using a documentclass{thesis}. It is a template I downloaded (http://www.latextemplates.com/template/masters-doctoral-thesis) and the chapters are compiled using macros. Everything was working perfectly until today, when suddenly the last two chapters no longer showed up as numbered chapters in the table of contents - thus resetting the section numbers in those (former) chapters, figure numbers, etc. The chapter titles and section titles still appear in the table of contents, and the text is correct, but the numbering has been messed up. I know that I could manually fix it using \setcounter (although when I do that, the number doesn't show up next to the chapter title in the table of contents), but I'd rather fix the problem. I disabled all the new packages one by one to see if one of those were interfering with the chapter number, but had no luck. I also deleted all the temporary documents from the folder I'm working in, restarted Texmaker, did a manually compile (rather than quick build) - all my normal go-to fixes for LaTex bugs. Has this happened to anyone before, and if so, any ideas on the fix? I even re-downloaded the template and fed my chapters back in, and the same problem happened - so I don't think I did anything in the LaTex Class document that contains the code.

Here are the packages I use. The rest of the main compiler page is specified by the template I downloaded. I don't know how to include a MWE in this case, as the document is extensive and the problem could potentially be anywhere. I was curious if this happened to anyone else, and if so, what kind of interference could cause it. I keep checking in chapter 2 to see if something in there interrupted the numbering before the document gets to chapter 3, but no luck yet. Thank you!

\documentclass[12pt, oneside]{Thesis}
\usepackage{etex}
\setlength\parindent{15pt}
\graphicspath{{Pictures/}} 
\usepackage[round, comma, sort&compress]{natbib}  
\hypersetup{urlcolor=black, colorlinks=true} 
\title{\ttitle} 
\usepackage{multirow}
\usepackage[table]{xcolor}
\usepackage{caption}
\usepackage{hyperref}
\usepackage[all]{xy}
\usepackage{multicol}
\usepackage{amsmath}
\usepackage{capt-of}
\definecolor{lightgray}{gray}{0.9}

closed as unclear what you're asking by Andrew Swann, Svend Tveskæg, Fran, Paul Gessler, user13907 Jan 1 '15 at 20:18

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

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    Before going crazy, delete all auxiliary files (.aux, .toc, .lof, .lot, ...) and try again. – Werner Dec 31 '14 at 22:19
  • Welcome to TeX.SX! You can have a look at our starter guide to familiarize yourself further with our format. – cfr Jan 1 '15 at 1:10
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    Comment stuff out. If the numbers disappear from chapter 3 onwards, comment out anything after chapter 3 and before chapter 2, along with as many packages as you can. Is the problem still there? If so, start commenting code in chapter 2. If you comment all of chapter 2, does chapter 3 get a number? If you comment half of chapter 2, does it? This is the only way to find the issue. Either you'll get an MWE you can post or you'll solve the problem. But try Werner's suggestion first. – cfr Jan 1 '15 at 1:12
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    Thanks for the comments - it was actually an extra } on a citation. The error was suppressed until I stripped it down - I wouldn't have found it otherwise. – Melissa Jan 2 '15 at 2:43