Comparing the following two files containing \intertext in align environment I obtain correct comparison for the first align environment and erroneous one for the second (with incorrect string \DIFadd{\intertext{whereas}):
file #1
\documentclass{article}
\usepackage{amsmath}
\begin{document}
First align environment:
\begin{align}
a&=b\
\intertext{whereas}
b&=c
\end{align}
Second align environment:
\begin{align}
a&=b\
\intertext{whereas}
b&=c
\end{align}
\end{document}
file #2
\documentclass{article}
\usepackage{amsmath}
\begin{document}
First ``align'' environment:
\begin{align}
a&=b\
\intertext{where}
b&=c
\end{align}
Second ``align'' environment is empty.
\end{document}
Probably the problem caused by the fact that the second align' environment in file #1 matches to nothing.
Comparing the following two files containing \intertext in align environment I obtain correct comparison for the first align environment and erroneous one for the second (with incorrect string \DIFadd{\intertext{whereas}):
file #1
\documentclass{article} \usepackage{amsmath}
\begin{document}
First align environment: \begin{align} a&=b\ \intertext{whereas} b&=c \end{align}
Second align environment: \begin{align} a&=b\ \intertext{whereas} b&=c \end{align} \end{document}
file #2
\documentclass{article} \usepackage{amsmath}
\begin{document}
First ``align'' environment: \begin{align} a&=b\ \intertext{where} b&=c \end{align}
Second ``align'' environment is empty.
\end{document}
Probably the problem caused by the fact that the second align' environment in file #1 matches to nothing.