Here is a short document demonstrating the problem:
\documentclass[twocolumn]{article}
\makeatletter
\renewcommand{\rmdefault}{ptm}
\renewcommand{\normalsize}{\@setfontsize{\normalsize}{9pt}{10pt}}
\makeatother
\usepackage[table]{xcolor}
\usepackage{amsmath}
\begin{document}
\begin{itemize} \item
\begin{align}
longfoo &\in foo \\
foo &= longlonglongfoo \\
foo &= foo && longlonglongfoo \\
\multicolumn{2}{c}{foo}
\end{align}
\end{itemize}
\end{document}
This produces a document that looks like this:
As you can see, the (4)
label does not line up with the others. I tried to minimize the document as much as possible, so the visual problem is not so serious in this small example, but you can see in my actual document that the alignment is quite far off indeed.
Why is the alignment off, and what can I do to fix it?