Hi Clinton,
I remember having some trouble when we didn't have these two present but I've had a brief look and I can't find the reason (it may be part of our Torque generation, which refers to log4j-1.2.8 but this is not required at runtime). I also don't like having the duplicates so we'll ensure they aren't there in the next release.
BTW.. I'm pretty certain you can run KonaKart fine without the 1.2.8 version... so just remove them from konakart and konakartadmin lib directories.
Thanks for your post,
Brian