Did what you recommended, and still no luck. Tried it 
on a isolated system, running Httrack 3.15.

Contents of /etc/httrack.conf (world-readable):
[smcphill@plinkcheck tmp]$ cat /etc/httrack.conf
# HTTrack Website Copier Settings
# See httrack --help for more information

set user-agent "Mozilla 4.5 (compatible; MSIE 5.5; 
PANDORA - National Library of Australia)"
# Deny and allow for links
# Beware! this will be used by default for all mirrors
deny pandora.nla.gov.au/*
deny www.nla.gov.au/pandora/*
r30

command-line used:
httrack -O /home/smcphill/tmp 
<http://cs.anu.edu.au/Student/comp3600>

this is a new project.
contents of hts-cache/doit.log:
[smcphill@plinkcheck tmp]$ cat hts-cache/doit.log
-O /home/smcphill/tmp 
<http://cs.anu.edu.au/Student/comp3600>
File generated automatically on Mon, 08 Apr 2002 
09:46:21, do NOT edit

To update a mirror, just launch httrack without any 
parameters
The existing cache will be used (and modified)
To have other options, retype all parameters and 
launch HTTrack
To continue an interrupted mirror, just launch httrack 
without any parameters

So it appears that the conf file is not being listened 
to at all, ever! If there's any other information I 
can send, please let me know.

system information: 
[smcphill@plinkcheck tmp]$ cat /proc/version
Linux version 2.4.7-10 
(bhcompile@stripples.devel.redhat.com) (gcc version 
2.96 20000731 (Red Hat Linux 7.1 2.96-98)) #1 Thu Sep 
6 17:27:27 EDT 2001