You always pay Karma. During chargen and after.
The (probable) intent is that you pay karma+nuyen only during post-chargen. However the rules don't do a good job of communicating whether you pay nuyen as well as karma during chargen. The rules don't mention it at all, but the chart does. So... meh.
Genesis doesn't force nuyen training costs for advancing skills, does it? If I may: I'd suggest treating martial arts as a karma-only forced expense, and letting players manually add a nuyen training expense. I mean, the GM might say the character's sensei gives them a price break for whatever reason, anyway. Or hikes the price...