make linux live scripts produce bootable iso

I'm trying to build an alpine linux and devuan live iso using linux live kit. I followed the instructions and everything seemd to be fine. However, both the resulting iso do not boot from the usb stick. I was able to boot the rootsfs in frugal mode and the iso from the hd using grub. I used dd to copy the iso to the usb, and I used the same process hundreds of times and iso always boot with no problem. This is the gen_mycd_iso.sh which linux live kit uses to produce the iso.

cd /mycd-data-4201 && /usr/bin/mkisofs \
  -o /tmp/mycd-x86_64.iso -v -J -R -D -A mycd -V mycd \
  -no-emul-boot -boot-info-table \
  -boot-load-size 4 -b mycd/boot/isolinux.bin \ 
  -c mycd/boot/isolinux.boot .

My guess is that somehow the script fails to write the correct bootable flag to the usb partition. Any suggestions as to how troubleshoot the issue?