If your 16 GB USB drive was formatted with the FAT32 file system then your persistent store may not be larger than 4 GB because there exists a limitation of the size of a single file. If you really need a larger persistent store then you have to use a file system like ext2 or Reiserfs. Don't use an NTFS formatted drive because there are people reporting that they got file system errors after having written on their drives from a Linux OS.

I think that the main difficulty in using a file system other than FAT or FAT32 is that you have to install the bootloader yourself instead of using the Knoppix Flash drive installer from the menu. You will need a bootloader like Grub(4dos) or extlinux.

I think that if you get the ADRIANE version after install then you can edit the file syslinux.cfg as described in post #10 of the thread http://www.knoppix.net/forum/threads...-Default-Login

I hope that helps although you didn't tell us what Knoppix version you are using.