I have found that for only one page (so far) the spacing between the header and content is different from the spacing on all the other pages. You can see this behavior in the images below (from pages 2 and 3 of the document):

My .tex file contents are shown below.
\documentclass[a4paper]{report}
\usepackage{fullpage}
\usepackage{lipsum}
\usepackage{fancyhdr}
\pagestyle{fancy}
\setlength{\headsep}{0.5cm}
\begin{document}
\renewcommand{\headrulewidth}{0.4pt}
\renewcommand{\chaptermark}[1]{\markboth{\thechapter. #1}{}}
\fancyhead[L]{\bfseries \leftmark}
\fancyhead[R]{\bfseries \rightmark}
\chapter{Version Control}
\lipsum
\lipsum
\lipsum
\lipsum
\end{document}
\My Subtitle. – Lev Bishop Aug 27 '10 at 03:04lipsumpackage. It makes minimal examples much smaller. – TH. Aug 27 '10 at 08:16lipsumpackage into the example. Thanks for the tip! – Ryan Taylor Aug 27 '10 at 12:17