Since upgrading to MacTeX 2016 the following example no longer compiles as expected:
\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage{amsmath}
\usepackage{breqn}
\begin{document}
\begin{align}
x &= y, && \text{(foo)}
\end{align}
\end{document}
with the text (foo) appearing a total of four times in four different sizes. The problem is due to the inclusion of breqn. Without using breqn, or if using a previous version of MacTeX, everything is as expected.
pdflatex, I see no unusual effects: The result of your document is the same with and withoutbreqn, namelyx=yfollowed by(foo)(once) followd by(1). Maybe add\listfilesat the beginning of the file such that we can compare the versions. – gernot Nov 19 '16 at 18:24(foo)... – gernot Nov 19 '16 at 18:26