I don't have an easy way to reproduce this, but I think I can explain it well
enough: In the class member view, see for example here
  http://dealii.org/developer/doxygen/deal.II/functions.html
functions and variables can start with '~' and ':' as well as underscores.
Doxygen generates individual pages for these which have names like
  functions_0x7e.html
When you click on the tabs with the letters and symbols (fourth level of the
menu at the top) you jump to a label of the form
  functions_0x7e.html#index_~
This label exists in the form
  <a class="anchor" name="index_~">
in file functions_0x7e.html in doxygen 1.5.6 from which the files for which
references are shown above were generated, but with doxygen 1.6.3 the anchor 
is escaped:
  <a class="anchor" id="index_0x7e">
In other words, while the href is not escaped, the anchor is, and the link
leads to nowhere.

The solution is of course to also escape the hrefs when referencing these
labels, or to not escape the anchors.

Thanks in advance
 Wolfgang