The programm confuses the base path file-pointer in 2 reproducable cases:

Windows XP, Httrack 3.47-24
Base path set to G:\siterip
Ususally my projects are stored in G:\siterip\<projectname>

1. I had some user preferences saved to G:\siterip-options
When I load these preferences using "Preferences - Load options" the whole
project will be stored in 
G:\siterip-otions\siterip\<projectname>

2. I had an URL list stored in
G:\siterip\URL-lists\<projectname>\URL-list.txt
When I enter this URL list reference in the field URL list, the whole project
will be stored in 
G:\siterip\URL-lists\<projectname>\siterip\<projectname>

So in both cases the base path is not handled as an absolute path reference
but somehow added to the path the program had worked in before.

If I put the respective files into the root directory G:\ everything works
fine, but that's only a workaround.

I had worked as a software developer myself, I'm curious how this turns out,
please let my know.