Comment 17 for bug 273023

Upon further study, I have further narrowed down the cause of the problem: The red boxes appear wherever there is a period character (.) when using Computer Modern fonts with certain font encodings. Here is a minimal example:

\documentclass{article}
\usepackage[T1]{fontenc}
\begin{document}
.
\end{document}

Add more periods to get more red boxes. The following font encodings produce red boxes:

T1
T2A
T2B
T2C
TS1
X2

The following font encodings do not produce red boxes (at least, not for the . character):

IL2
LCY
LGR
LMC
LO1
LY1
OML
OMS
OT1
OT2
OT4
T2D
T3
T4
TS3