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I am writing my thesis with pdflatex and did not have any problems until now. When I compile my thesis I don't get any errors. However a part of a sentence is suddenly missing (so that a part of a line is just blank). I was trying to locate what the reason for this is, and it seems to be that if I remove one or two words in the last sentence of the paragraph (or somewhere else), the text looks fine. Does anyone have any idea why this is happening? All references are fine and everything compiled just fine yesterday. Today I added some minor corrections from my professor and this suddenly happened.

If I compile the same paragraph separately with the same preamble, I don't get this problem.

I attached two images, to illustrate the problem:

Compiling in Document:

Compiling in Document

Compiling Separately:

enter image description here

If a MWE example helps, I can do that, but obviously everything works, the text is just radomly missing...

Here is a more or less minimal working example:

% % % % % % % % % % % % % % %
\documentclass[a4paper,
final,
12pt,
numbers=noendperiod, 
BCOR=5.00mm,
bibliography=totoc,
listof=totoc]{scrreprt}


\usepackage[english]{babel}
\usepackage{tocbasic}
\usepackage{scrhack}
\usepackage[toc,page]{appendix}


\usepackage[usenames,dvipsnames,svgnames,table]{xcolor}




\usepackage[right]{eurosym}

% Font Encoding 
\usepackage[T1]{fontenc}
\newcommand{\changefont}[3]{
\fontfamily{#1} \fontseries{#2} \fontshape{#3} \selectfont}



\usepackage[utf8]{inputenc}


\usepackage{libertine}
\usepackage[scaled=.83]{beramono}
\usepackage[libertine]{newtxmath}
\DeclareMathSymbol{=}{\mathrel}{operators}{`=} % redefine math for chemmacros
%\usepackage{eulervm} % Math typing
\usepackage{microtype}



\usepackage{csquotes}
\usepackage[backend=biber,style=chem-angew]{biblatex}
\addbibresource{acf.bib}


\usepackage{longtable}
\usepackage{graphicx}

% mehrere Spalten vereinigen
\usepackage{multirow}

% Better table layouts
\usepackage{booktabs,dcolumn}

% Paket für Zeilenabstand
\usepackage[onehalfspacing]{setspace}



\usepackage{tabularx}



\frenchspacing


% Mathematische Sachen
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amstext}
\usepackage{mathtools}
\usepackage{bm}
\usepackage{nicefrac}
\usepackage{braket}
\usepackage{environ}
\usepackage{tikz}
\usetikzlibrary{calc,arrows}
\usepackage{tabulary}
\usepackage{pdflscape}


\usepackage{graphicx}

\usepackage{siunitx}

\usepackage{xspace}




%%\usepackage{overpic}
\newcommand{\pnmr}{\textsuperscript{31}P-NMR\xspace}
\newcommand{\phnmr}{\textsuperscript{31}P\{\textsuperscript{1}H\}-NMR\xspace}
\newcommand{\hnmr}{\textsuperscript{1}H-NMR\xspace}
\newcommand{\cnmr}{\textsuperscript{13}C-NMR\xspace}
\newcommand{\cnmrh}{\textsuperscript{13}C\{\textsuperscript{1}H\}-NMR\xspace}
\newcommand{\engl}{\textit{engl.}\xspace}
\newcommand{\etal}{\textit{et al.}\xspace}
\newcommand{\via}{\textit{via}\xspace}


\newcommand{\M}{[M]\textsuperscript{+}}
\newcommand{\MH}{[M+H]\textsuperscript{+}}

\newcommand{\superscript}[1]{\ensuremath{^{\textrm{#1}}}}
\newcommand{\subscript}[1]{\ensuremath{_{\textrm{#1}}}}

\usepackage[within=chapter]{newfloat}


\DeclareFloatingEnvironment[
fileext=los,
name=Scheme,
listname={List of Schemes},
]{scheme}


\usepackage{caption}
\usepackage{subcaption}
\captionsetup{format=plain,
font=onehalfspacing,font=footnotesize}
\captionsetup[table]{belowskip=2ex}


\captionsetup[sub]{font+=footnotesize}


\usepackage{multicol}
\newcolumntype{.}{D{.}{.}{-1}}


\usepackage[version=3]{mhchem} % Formula subscripts using \ce{}
\usepackage{bpchem}
\usepackage{psfrag}
\usepackage[crop=off]{auto-pst-pdf} % Use EPS graphics with pdfLaTeX
\usepackage{xkeyval}
\usepackage{pst-pdf}
\usepackage{ifplatform}
\usepackage{chemnum}
\cmpdsetup{cmpd-style =\rmfamily, ref-style = \rmfamily}
\usepackage{chemgreek}




\setkomafont{captionlabel}{\sffamily\bfseries}

\usepackage{lipsum}

% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % %
% Automatic List of Abbreviations % % % % % % % % % % % % % %
% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
\usepackage{nomencl}
\makenomenclature
\renewcommand*{\nomprefix}{}
\newcommand*{\nom}[2]{#1\nomenclature{#1}{#2}}
\renewcommand{\nomname}{Abbreviations}
\renewcommand{\nompreamble}{\markboth{\nomname}{\nomname}}
% % latex run, then use nomencl command, then run latex again

% % % % % % % %Header % %
\pagestyle{headings}
%\setcapindent{1.5em}

% % % % % % % % % % % % % % % % % % % % % % % % % %
%Hyperref % % % % % % % % % % % % % % % % % % % % %
% % % % % % % % % % % % % % % % % % % % % % % % % %

%\usepackage[linktocpage=true]{hyperref}
\usepackage[bookmarksnumbered,hyperfootnotes=false,breaklinks=true]{hyperref}
\hypersetup{colorlinks,
            citecolor=DarkGreen,
            linkcolor=black, %DarkBlue,
            urlcolor=black} % % Bestimme Farben von Hyperrefverweisen

\KOMAoptions{DIV=last}

\begin{document}

The structures of these PN ring systems have been extensively studied in the solid state
\via single crystal X\mbox{-}ray crystallography, where in a predominant number of cases
only the thermodynamically favoured \textit{cis} isomers can be observed. 

\pnmr experiments on the other hand suggest that both \textit{cis} and \textit{trans}
species can be encountered in nearly equal amounts in solution.\supercite{Stahl2000}

Although there is a general consensus in the literature that the \textit{cis} isomer is 
the more stable product, little is known about the reasons for this trend.

Low\mbox{-}level \textit{ab\mbox{ }initio} and semi\mbox{-}empirical calculations 
presented by Haiduc and co-workers in 1994 provide insight into the source of puckering,     
but fail to explain observed stabilities.\supercite{Silaghi-Dumitrescu1994}

Another related facet of cyclodiphosphazane chemistry that has received little attention
is the mechanism of ring inversion, where vertex inversion at the phosphorus, edge   
inversion at the imino nitrogen and a sequence of cycloreversion and cycloaddition have     
been proposed.\supercite{Chen1985,Wirringa1995,Silaghi-Dumitrescu1998,Schranz1999} %,  

     \end{document}
26
  • 1
    What is the result, if the file is viewed in a different PDF viewer? Apr 7, 2014 at 12:33
  • 1
    ... which could also be an indicator that possibly something is not as it should long before the compiler reaches that location. I've seen similarly mysterious things happen out of presumably valid sources which compiled without the slightest warning, but there was a missing bracket or erroneous equation/math or what not long before the location at which problems visually occured in the output document. Apr 7, 2014 at 12:56
  • 3
    Please take your first example (with the error), than delete all the text after that. Check if the error persist. Than delete half of the text before the error. If the error is still there, do it again, and so on. Like this, you can reduce the code. If you are done, minimize the number of packages the same way.
    – LaRiFaRi
    Apr 7, 2014 at 13:03
  • 1
    The behaviour of TeX can be quite unpredictable if it tries to plough through errors, so I thought this might be the problem. If you don't have any errors elsewhere in the document, I have no idea what's going on. Apr 7, 2014 at 13:36
  • 1
    Nice to read that you were able to solve it. As it's a bit unclear (and solved) I closed the question. You can still comment or vote to reopen if you would like to write an answer.
    – Stefan Kottwitz
    Apr 8, 2014 at 8:22

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