> (winhttrack
> -qgr2C2%Pns2u1%s%u%I0p3DaK0H0%kf2A25000%f#f -F
> "Mozilla/4.5 (compatible; HTTrack 3.0x; Windows 98)"
> -%F "<!-- Mirrored from %s%s by HTTrack Website
> Copier/3.x [XR&CO'2008], %s -->" -%l "en, en, *"

You previously said you are using site structure.
The flag for site structure is -N0
No such flag is listed in the log.
My mirror's doit.log contains:
-qwr4%e0C2%PnxX0s0u1Z%s%uN0%I0p3DaK0c9T60J99R9H3%kf2o0A97280%c5%f#f
...<%u><N0><%I>... Check your settings.
I didn't think this was possible from the GUI. You might have to set it to
something else, save but don't launch, and then change back.