In my recent builds of the html documentation (sphynx 1.1.3, numpydoc 0.4) I have
noticed 2 issues (And thanks to @NelleV online builds, I know that I am at
least not the only one):

• 2 modules links appears in the top toolbar (on the left), for 2 domains
  py-modindex and np-modindex (which in fact are identical).
  If I am correct, this is related with sphynx new keyword
  http://sphinx-doc.org/config.html?highlight=html_use_modindex#confval-html_domain_indices
  Explicitely setting html_domain_indices = ["py-modindex"] in the build
  configuration file config.py (line 162) seems to solve this.
• The "previous topic", "next topic" sometimes (often) disappear. Compare for instance
  http://matplotlib.org/api/ticker_api.html#module-matplotlib.ticker with
  http://cbio.ensmp.fr/~nvaroquaux/matplotlib/doc/api/ticker_api.html#module-matplotlib.ticker
  It seems that some prev-next relationships are no more included in the sphynx toc tree ; however this goes far beyond my understanding of the doc build.