The output of pdflatex has changed between TeX Live versions 2013 and 2014. A minimal example:
\documentclass[11pt,a4paper]{article}
\usepackage[papersize={104mm,16mm},vmargin=2mm,hmargin=2mm]{geometry}
\usepackage[T1]{fontenc}
\usepackage[charter]{mathdesign}
\usepackage{microtype}
\thispagestyle{empty}
\begin{document}
x xxxxxx xxxxxx xxxxxx xxxxxx xxxxxx xxxxxx xxxxxx xxxxxx xxxxxx xxxxxx
\end{document}
Compiled with pdflatex from MacTeX 2013 (TeX Live 2013):

Compiled with pdflatex from MacTeX 2014 (TeX Live 2014):

In the first case, pdflatex is happy. In the second case, there is an overfull hbox. The relevant versions are:
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
LaTeX2e <2011/06/27>
geometry 2010/09/12 v5.6
microtype 2013/05/23 v2.5a
mathdesign 2006/01/29 v1.55
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014)
LaTeX2e <2014/05/01>
geometry 2010/09/12 v5.6
microtype 2013/05/23 v2.5a
mathdesign 2013/08/29 v2.31
What has changed and why? Can I somehow use TeX Live 2014 in a backwards-compatible mode so that it does not change the layout of my documents?
mathdesignin TL 2013 is ancient; my TL 2013 has v. 2.31. So I suspect this is the issue. – Alan Munn Aug 01 '14 at 19:31