How to \label and get recognised?

Question

This issue actually frustrates me for a while, but prior for finding the solution, I would like to know why this happens. In a nutshell: My TeXStudio does recognise ALL my \label, but the output does not recognise some labels.

Problem

I am writing my notes on Physics, however, sometimes I got warnings of:

LaTeX Warning: Reference `eq:pointcd' on page 196 undefined on input line 985.

This is just for example, I have other examples in the document that does not have \label recognised. There are also some weird situation where I have the same format of putting \label, but got recognised by the compiler.

MWE

\documentclass[12pt,a4paper,headinclude,openright]{scrbook}
\usepackage{amsmath}
\usepackage{amssymb}
% ------------here comes the problem part------------
\usepackage[listings,theorems,skins,breakable]{tcolorbox}
\tcbuselibrary{breakable}
%======================== Ch.4 boxes =========================
\tcbset{exercisestyle04/.style={arc=0.5mm,coltitle=black,fonttitle=\sffamily\bfseries,colback=color04!50!,colframe=color04}}

\newtcolorbox[auto counter,number within=chapter,list inside=eg]%
{exercise04}[2][]{exercisestyle04,
title={Exercise ~\thetcbcounter: #2}}

\tcbuselibrary{theorems}
\usepackage[amsthm,thmmarks,hyperref]{ntheorem}
% theorem 
\usepackage{regexpatch}
\makeatletter
\xpatchcmd*{\thm@@thmline@name}{2.3em}{5em}{}{} 
\xpatchcmd*{\thm@@thmline@noname}{2.3em}{5em}{}{}
\makeatother
\makeatletter
\renewtheoremstyle{plain}%
{\item[\hskip\labelsep \theorem@headerfont ##1\ ##2 \theorem@separator]}%
{\item[\hskip\labelsep \theorem@headerfont ##1\ ##2\ \sffamily{##3}  \theorem@separator]}
\makeatother
\theoremstyle{plain}
\theorembodyfont{\normalfont\sffamily}
\theoremheaderfont{\bfseries}
\newtheorem{theorem}{Theorem}[section]
% ------------here ends the problem part------------
\begin{document}
\begin{equation}
\rho\left(\mathbf{r}\right)\;=\;\sum_{k=1}^{N}\: q_k \delta\left(\mathbf{r}\;-\;\mathbf{r}_k\right)
\label{eq:pointcd}
\end{equation}
However, one should alert for the unphysical divergence in other quantities associated with \eqref{eq:pointcd}.
\end{document}

In your answer...

I am not specifying you of how to answer this question, this section is just my suspects on the issue. For example,

1. The pdf compiler is faulty? (I use Acrobat XI and with PdfLaTeX as compiler and using DVI -> PS -> PDF chain in TeXStudio)
2. My compiling procedures has done wrongly?
3. My format is done wrong (although I fairly think so because I changed my format according to many sources but no luck).
4. TeXStudio is faulty? (Just a suspect, but did happened with other IDEs before and I am using ver. 2.8.0)
5. I haven't read the manual carefully? (smile)

It turns out some code has obstructed the PdfLaTeX to recognise some \label.

Update

While I was omitting the parts that I have some idea why it happens, however, it is neither of the five above.

1. While I deleted some of the \frontmatter, by delete a section (see MWE above) become fine to recognise the referencing.
2. I suspect the part is obstructing the compiler to recognise some \label.

Solution

See Mico's answer, but I would like to append that it was actually because of

5. I haven't read the manual carefully

Answer 1

Thanks for posting some code that produces the problem behavior you're looking to solve.

The problematic statement in your preamble turns out to be

\usepackage[amsthm,thmmarks,hyperref]{ntheorem}

and, more specifically, the option thmmarks. Remove this option, and the cross-referencing problem goes away.

Alternatively, since you load the amsmath package as well, simply add the option amsmath and the thmmarks option doesn't cause problems either. (Incidentally, this fix is mentioned explicitly in section 3.2.1 of the user guide of the ntheorem package.)

\usepackage[amsthm,amsmath,thmmarks,hyperref]{ntheorem}