Cannot generate bibliography using TeXworks from MiKTeX

Too long for a comment: Let's try us another way. Can you please compile the following MWE on your system? It works for me with pdflatex -- bibtex -- pdflatex -- pdflatex.

%File mb-bibtex.tex, then \jobname = mb-bibtex
\RequirePackage{filecontents}        % loading package filecontents
% writing file \jobname.bib, for example mb-bibtex.bib.
\begin{filecontents*}{\jobname.bib}
@Book{companion,
  author    = {Goossens, Michel and Mittelbach, Frank and Samarin, Alexander},
  title     = {The LaTeX Companion},
  edition   = {1},
  publisher = {Addison-Wesley},
  location  = {Reading, Mass.},
  year       = {1994}
}
@Book{adams,
  title     = {The Restaurant at the End of the Universe},
  author    = {Douglas Adams},
  series    = {The Hitchhiker's Guide to the Galaxy},
  publisher = {Pan Macmillan},
  year      = {1980}
}
\end{filecontents*}


\documentclass{article}

\usepackage[numbers]{natbib}         % bibliography style
\usepackage[colorlinks]{hyperref}    % better urls in bibliography

\begin{document}
Test of bibliography: 
The \LaTeX{} companion~\cite{companion}, the funny book of Adams~\cite{adams}.

\bibliographystyle{plainnat}  % needs package natbib
\bibliography{\jobname}       % uses \jobname.bib, according to \jobname.tex
\end{document}

To be sure (that there is no error in your config of your editor) please use the terminal/console.

I had the exact same problem, and I was finally able to diagnose and solve my problem. I am posting so others may find this potential problem as I have not seen this as a solution to this problem.

I am working on a Windows 7 machine (ugh--it's my office's requirement). After an hour+ of trouble shooting, I found my problem was the file type of my .bib file. I had exported from Endnote to bibtex (or so I thought). Endnote made a .txt file. I manually changed this to a .bib file.

However, the file was actually just retitled myLib.bib.txt. Yuck.

When I opened my myLib.bib.txt in JabRef and did a "SaveAs" choosing .BIB fileType, everything finally worked. I did the normal:

1. pdfLatex myFile.tex
2. bibtex myFile.aux
3. pdfLatex myFile.tex
4. pdfLatex myFile.tex

Again, now everything worked. It was a filetype error that was leading to an empty .bbl file. When I say empty, previously my .bbl file had only the \begin and \end lines, with no actual content.