Something tells me that I should reply to this thread but the trouble is I don't know how because the information is too sketchy.
I entered Linux in June 2004 and have not had a need to do a mkboot. I believe that is old school when Linux had to be booted with the assistance of a Dos partition. I believe you are following some ancient howto trying to boot Linux from the real Dos mode off Win9x.
If the mkboot is indeed a workable solution then a floppy image would have been downloadable from the Knoppix site.
I believe your ambition is better served with Grub4Dos. It is a version of Grub installable in a Dos partition or SuperGrub that supplies a downloadable floppy image. Once a bootable floppy image, from either source, has been made then you will be in a position to run/boot Grub. Grub can boot up any kernel you have inside Win9x.
My problem is that the way you seem to run Linux is out of date. Running a Linux from a Win9x partition was done with Loadlin was the Linux boot loader and hard disks did not cross 1024 cylinders barrier.
Nowaday everybody download an iso, burn it into a bootable CD, boot up the CD and the Linux will be installed into the memory. We can then run it as a Live CD, satisfied with it before make the decision to install it into the hard disk. We dive head first into 100 to 500Gb hard disks and working only with Linux-specific Ext2/3 and Rieserf partitions.
If you can't boot up a CD then you are denied access to the majority of the distros and may have a long road to get to what everybody is doing now in LInux. It can be done but a fair amount of skill is needed and you are not severely handicapped by starting from a Win9x partition without a bootable CD rom.