After a recent update from MacTex 2015 to 2016, the forest package also updates, which caused problems for an existing tree had. The problem concerns the example number the gb4e package creates. Before the update the number appeared at the same height as the node CP-phase. In this version the example number appears at the bottom.
\documentclass{minimal}
\usepackage{forest, gb4e}
\forestset{
fairly nice empty nodes/.style={
delay={where content={}{shape=coordinate,for parent={
for children={anchor=north}}}{}}
}}
\useforestlibrary{linguistics}
\forestapplylibrarydefaults{linguistics}
\begin{document}
\begin{exe}
\ex \label{saktree1}
\begin{forest}, fairly nice empty nodes,
[CP-phase, phantom, l sep=19pt,
[\ldots, for descendants={l=0}, name=dots, tikz={\node [draw,inner sep=20pt, fit=(V)(dots)(book)(Erel)(v)(T)] {};}
[\textit{v}P
[DP
[Erel, fit=band, roof, name=Erel ] ]
[{}, calign angle=60
[VP, name=VP, tikz={\node [draw, inner sep=1pt, fit=(VP)(V)(book)] {};}
[DP
[ kinige, name=book, roof ] ]
[V\\atyylas-ta, name=V] ]
[\textit{v}, name=v, fit=band ] ] ]
[T, name=T, fit=band ] ] ]
\node at (dots)[above=6ex]{\bfseries{CP-phase}}; baseline
\node at (VP)[below=78pt]{\bfseries{VP-phase}}; name=VPnod
\end{forest}
\end{exe}
\end{document}
The code yields the following output:

phantomnode is drawn; if you remove that, it aligns again. (Not a solution, just an observation.) The code for this was changed in the most recent version, so possibly this is a bug. – Alan Munn Aug 08 '16 at 22:34phantommakes part of the problem go away, but the example number shows up at the same height as the three dots node and not att the CP-phase node. – David Kroik Aug 08 '16 at 22:49phantomfrom your code and make the\node...command that contains CP phase empty, the number lines up with the CP phase node. – Alan Munn Aug 08 '16 at 22:52