I think the problem is that I either didn't alter /boot/isolinux/*cfg correctly(I left the one that has default auto near the top unaltered
Hello Jeffery!

At the end of
http://knopper.net/knoppix/knoppix760-en.html
you'll find
<cite>
Boot options like "adriane" can easily be preset by changing syslinux.cfg after having copied the CD to a bootable memorystick using "flash-knoppix": Update: Computers without DVD driveChange the upper line
DEFAULT auto
to:
DEFAULT adriane
for automatically starting ADRIANE on boot. This is already default in all ADRIANE iso files.
</cite>

Why do you use this painful way to rebuild the image with genisoimage instead of doing a Flash install. Within the link i've mentioned above you can also see at the position
→ Update: Computers without DVD drive
how to do the Flash install using tje command line.