Having the same problem. URL's are of the form:
  <http://localhost:4000/PmWiki/index.php?n=Projects.Main>

Options are set to:
  %h%p/%[n::_::]%n%q.%t

And I end up with files named:
  pmwiki\localhost_4000\PmWiki\index9696.html

What I want to end up with:
  pmwiki\localhost_4000\PmWiki\Projects.Main_9696.html