The microtype package (or more likely the pdfTeX microtypographic extensions) have a strange interaction with \parindent that bit me.
\documentclass{article}
\usepackage{microtype}
\begin{document}
0:\vrule\strut\par
1:\vrule\strut\par
\parindent0pt
0:\vrule\strut\par
1:\vrule\strut\par
\microtypesetup{protrusion=false}
0:\vrule\strut\par
1:\vrule\strut\par
\end{document}

The colon after the second 1 is typeset slightly to the left of the one after the 0, but only when microtype's protrusion is on and \parindent is 0. Indeed, changing the \parindent to .00001 pt causes the rules to line up.
This seems like a bug to me, but it's possible that I just don't understand what is supposed to happen here.
The two work arounds are to either disable protrusion where I need this to line up, or change the \parindent to a small, nonzero value. Is there a better option?
microtypeand\parindent.\parindentis set to 0, thenmicrotypeapplies margin kerning, so that the1will slightly protrude into the left margin. Of course, it's debatable whether the same thing should not also happen when\parindentis said to 0.00001pt.microtypeand indentation (or the lack of), and that {indentation} is a proper tag. Whether an extra {parindent} tag is needed is open to debate. Also note that concept tags are preferred to command tags.