I recently (foolishly) updated all my TeXlive packages, including pgfplots (from 1.10 to 1.11).
I now have an issue with the groupplots and fillbetween libraries, where using the fillbetween library 1) doesn't work and 2) breaks the alignment of the group plots.
MWE:
\documentclass{article}
\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{compat=1.11}
\usepgfplotslibrary{fillbetween,groupplots}
\begin{document}
\begin{tikzpicture}[trim axis group left]
\begin{groupplot}[%
group style={%
group size=1 by 2,
vertical sep=0pt,
x descriptions at=edge bottom},
width=11.5cm,
scale only axis,
xmin=-1.8,
xmax=1.8,
/pgf/number format/use comma,
xlabel={Y [mm]},
]
\nextgroupplot[height=2.49166666667cm,ylabel={Z [mm]},y label style={at={(axis description cs:-0.08,.5)}},ymin=-0.59,ymax=0.19]
\nextgroupplot[ylabel={$\kappa$ [mm$^{-1}$]},y label style={at={(axis description cs:-0.08,.5)}},ymin=-12,ymax=8,height=6cm]
\addplot[color=green,solid,name path=mittemin] coordinates {(-1.8,-10) (1.8,-10)};
\addplot[color=green,solid,name path=mittemax] coordinates {(-1.8,-1.5) (1.8,-1.5)};
\addplot[color=green,solid,name path=randmin] coordinates {(-1.8,0.9) (1.8,0.9)};
\addplot[color=green,solid,name path=randmax] coordinates {(-1.8,6.5) (1.8,6.5)};
\addplot[green!20] fill between[of=mittemin and mittemax];
\addplot[green!20] fill between[of=randmin and randmax];
\end{groupplot}
\end{tikzpicture}
\end{document}
This yields the following result (no filling, broken alignment):

After commenting out the (non-functioning) fill between statements, the alignment is right again:

This hasn't occurred with pgfplots 1.10. Setting compat=1.10 does not change the output. As far as I can work out, something was changed in the fillbetween library for 1.11, is this a bug or am I missing something?
EDIT:
I downgraded to pgfplots 1.10, which fixed the problem (for anyone with the same issue: uninstalled the old version via tlmgr, downloaded it here, unzipped it to TEXMFLOCAL and ran mktexlsr). The issue therefore seems to be related to pgfplots only, I am going to ask Christian Feuersänger about it.
anchor=southto the groupplot options. Filling requires some more investigation indeed. – percusse Sep 15 '14 at 09:41