Are there any dependencies causing my \ref to not compile?

Question

I have learned that for labels and their respective references to compile and display correctly (for figures), it is necessary to have the \label{} after \caption{}, such as below:

Figure \ref{k2a}

\begin{figure}[h]
 % \caption{Isothermal thick film.}
  \begin{center}
    \centering
    \includegraphics[width= \columnwidth]{/home/userid/Research/Dissertation/2D/Periodic/k2a}
     \caption{When $\lambda = \lambda_{max}$ and M=35.1, Pr=7.20, S=100, G=1/3, rupture takes place at t=1280.0 (within 1\% or\citet{Krishnamoorthy1995a})}
     \label{k2a}
  \end{center}
\end{figure}

However, are there any .sty / package dependencies that are not allowing my labels to compile right? I run latex twice but I receive a bunch of warnings such as Reference on page abc undefined on input line xxx. and I get the dreaded ? where the reference should be. The link to the figure through the question mark works though.

Here is my preamble, where I load all my packages. This occurs in a separate file.

does \usepackage{caption} have anything to do with this issue?

\usepackage{graphicx}
%\usepackage{float}
\usepackage[section]{placeins}    
\usepackage{caption}
\captionsetup{margin=10pt,font=small,labelsep=period,labelfont=bf}
% --------
\usepackage{lscape}         % allows for landscape tables and figures
\usepackage{paralist}       % enancements to list environment
\usepackage{array}          % enhancements to array and tabular environments
\usepackage[usenames]{color}    
\usepackage{url}            
\usepackage{longtable}      % multipage tables
\usepackage{ifthen}
\usepackage{ifpdf}
\usepackage{setspace}       % easy single or doublespacing
\usepackage{amsmath,amsfonts,amssymb}
\usepackage{rotate}
\usepackage{subfigure}
\usepackage{subfig}
\usepackage{wrapfig}
\usepackage{listings}       % for listing computer code such as matlab
\usepackage[bw]{mcode}      % for matlab code with listings package
\usepackage[square,comma,sort&compress]{natbib} % enhances bibtex citations
% \usepackage{biblatex}
\usepackage{setspace}       % \singlespacing, \onehalfspacing, \doublespacing, ...

%%%%%%%%xyz%%%%%%%%%%%%%%%
\usepackage{epsfig}
\usepackage{epstopdf}
\usepackage{textcomp}
\usepackage{multirow}
%\usepackage{subfig}
\usepackage{paralist}
\usepackage{changepage}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%11022012-START%%%%%%%%%%%%%%
\usepackage[T1]{fontenc} %Useful for file names with underscores in them
\usepackage{float}
\usepackage{grffile}
\newcommand{\hilight}[1]{\colorbox{yellow}{#1}} %To highlight text
\renewcommand{\thefootnote}{\alph{footnote}} %For footnotes
%%%%%%%%%%11022012-STOP%%%%%%%%%%%%%%

Answer 1

As mentioned in the comments, it is very useful to provide a minimum working example (MWE) rather than copying your entire preamble (you did not include the documentclass in your code, but that's important).

For example, the following compiles fine with LaTeX.

\documentclass{article}

\usepackage[T1]{fontenc}

\usepackage{caption}
\captionsetup{margin=10pt,font=small,labelsep=period,labelfont=bf}

\begin{document}

Figure \ref{k2a}.

\begin{figure}[htp]
    \centering
%     \includegraphics[width= \columnwidth]{/home/userid/Research/Dissertation/2D/Periodic/k2a}
     \caption{When $\lambda = \lambda_{max}$ and M=35.1, Pr=7.20, S=100, G=1/3, rupture takes place at t=1280.0}
     \label{k2a}
\end{figure}

\end{document}

Incidentally, your entire preamble compiles fine on my machine with the caption package and the undefinend reference errors only occur because I don't have your citations.

A few other things, mentioned in the comments above and summarised here:

• Load graphicx instead of epsfig
• Load xcolor instead of color
• Load only subfig and not the depreciated subfigure
• You load setspace twice
• Don't use the center environement in the float. centering is enough
• Don't use [h] for placement unless you really need to, in which case [h!] is preferred (I think). Otherwise use something like [htbp], which instructs LaTeX to try an place the float here, top, bottom, page in that priority.

The l2tabu document might provide an interest read, which discusses some of LaTeX' obsolote packages and options.