If however I type modprobe snd-seq in a terminal qjackctrl works perfectly with no errors afterwards. I'd just like to have it automatically load at boot time(snd-seq).
You could try to "save configuration" which will create a knoppix.sh file on some hard disk. Then edit the knoppix.sh file to include a "modprobe snd-seq" line at the end. On reboot, issue the cheat code "knoppix myconfig=scan". Knoppix will then scan you disks for the knoppix.sh file and execute the knoppix.sh script, which should include running the modprobe command you want.