> IMHO, the fix would be to update the command line 
> options in 'doit.log' and not simply append them.

Hum, this is a problem.. when you are updating, you 
should use only 'httrack --update', and not list all 
options, because the update/continue process 
automatically reads the doit.log file to catch all 
previous options. This allow to keep all filters and 
settings without having to retype them.

When you want to retype ALL options, ensure that you 
also type all URLs - HTTrack will detect that you 
entered URLs, and will wipe all previous options. But 
entering only few options, without URLs, will force 
HTTrack to reload the previous ones!

Therefore, use either:
httrack --update
or
httrack --update www.foo.com -c1 -<other options>..