The following MCE points out an extra vertical space before display equations in case of fleqn option given at \documentclass level.
Do you know what's going on?
% Workflow if this file is named `test.tex`:
% pdflatex test
% pdflatex without-fleqn
% pdflatex with-fleqn
%
\begin{filecontents*}{without-fleqn.tex}
\documentclass{article}
\input{maths}
\end{filecontents*}
\begin{filecontents*}{with-fleqn.tex}
\documentclass[fleqn]{article}
\input{maths}
\end{filecontents*}
\documentclass{article}
\usepackage{filecontents}
%
\begin{filecontents*}{maths.tex}
\usepackage[papersize={15cm,3cm}]{geometry}
\usepackage[step=1cm]{pagegrid}
\usepackage{amsmath}
\begin{document}
Foo :
\[
y=Ce^{-\int a(x)dx}\int b(x)e^{\int a(x)dx}dx
\]
\end{document}
\end{filecontents*}
%
\begin{document}
\end{document}



amsmath)? – touhami Mar 28 '18 at 19:09gatherenvironment instead of\[...\](orequationenvironment) does the trick, but still strange. I guess this is a bug (maybe the same as in this question/answer). Should it be reported? – Denis Bitouzé Mar 28 '18 at 19:17amsmath? – touhami Mar 28 '18 at 20:17amsmath.\[and\]are redefined inflqn.cloand so doamsmath.sty. – touhami Mar 28 '18 at 20:26amsmath;) But at least it could fix the problem :) – Denis Bitouzé Mar 28 '18 at 20:29