If you're using an alternative templates path in your global hgrc file, the hgwebdir class doesn't use this configuration and still displays the index file with the default template. I have created a patch, which should resolve this problem.
Hmm, looks good to me.
Patches go to mercurial-devel@selenic.com.
Fixed by http://hg.intevation.org/mercurial/crew/rev/48163c39e1f1 (hgwebdir: use template paths configured in the hgrc (issue2281))
--- Bug imported by bugzilla@serpentine.com 2012-05-12 09:10 EDT --- This bug was previously known as _bug_ 2281 at http://mercurial.selenic.com/bts/issue2281 Imported an attachment (id=1432)