The last line before the first equation ends with a space. This is usually not a problem,
because TeX ends the text before the displayed equation similar to a paragraph end. That means, the last space is removed and \parfillskip is added.
However, package hyperref has to insert whatsits somewhere at some time. It hooks into \refstepcounter, that is called right before displaying the equation to update the
equation counter. hyperref uses this to add an anchor that is needed as link target,
if the equation if referenced.
However, then the last space of the previous text cannot be removed, because the whatsit/anchor goes inbetween, hiding the space. Because the text fills the previous line, the result is a line break, followed by an invisible line with the anchor. The space is removed at the start of the new line, but the invisible line remains, consuming space.
As quick workaround, the space can be removed by a percent line:
...aemm%
\begin{equation}
Better is a fix that does remove the space automatically and fixes the position of the anchor, because the position at the end of the previous line is not a good place.
\documentclass[12pt,fleqn]{book}
\usepackage{amsmath}
\usepackage[colorlinks]{hyperref}
\usepackage{etoolbox}
\makeatletter
\patchcmd{\equation}{\incr@eqnum\mathdisplay@push}{%
\ifhmode
\unskip
\vadjust{%
\incr@eqnum
\global\let\gfix@incr@eqnum\incr@eqnum
\global\let\gfix@currentlabel\@currentlabel
\global\let\gfix@currentHref\@currentHref
}%
\let\incr@eqnum\gfix@incr@eqnum
\let\@currentlabel\gfix@currentlabel
\let\@currentHref\gfix@currentHref
\else
\incr@eqnum
\fi
\mathdisplay@push
}{}{}
\makeatother
\begin{document}
\chapter{plo}
\section{plo}
eoiu oieu oeiuoe ueoi ueoi ueoiu eoiu oeu oe iupaêio umùaeoiuaem oeiu eoiu
eoiu oeee.
eoiu oieu oeiuoe ueoi ueoi ueoiu eoiu oeu oe iupaêio umùaeoiuaemm
\begin{equation}
\label{eq:first}
\cos\pi=-1
\end{equation}
eoiu oieu oeiuoe ueoi ueoi ueoiu eoiu oeu oe iupaêio umùaeoiuaem oeiu eoiu
eoiu oeee.
eoiu oieu oeiuoe ueoi ueoi ueoiu eoiu oeu oe iupaêio umùae
\begin{equation}
\label{eq:second}
\cos\pi=-1
\end{equation}
Equations \ref{eq:first} and \ref{eq:second}.
\end{document}

:? – Sigur Jul 03 '13 at 21:59\gluelines? – pluton Jul 03 '13 at 22:17\showoutput– David Carlisle Jul 03 '13 at 22:18\glue(\baselineskip) 12.16669. – egreg Jul 03 '13 at 22:20