When I generate a .pdf file from a .tex file using pdflatex, only the "Contents" title is shown with no actual TOC. If I run pdflatex my.tex once more, it generates the TOC just fine. I can reproduce this simply by removing the .toc file. What I think is happening is that my .toc file is being generated too late -- so how can I make the TOC work first time? Should I be generating the TOC beforehand without using pdflatex?
This is normal. LaTeX document need several compilations to reach a stable state. Use rubber -d my to compile the right number of times (rubber comes as a package on many linux distros).