FWIW, the host system is a 32-bit P4 with Hyperthreading enabled. I went through everything again by booting the system with the original Knoppix 6.2.1 disk and testing the resulting .iso with QEMU.

One thing to note is that there was no .rr_moved file/folder in the source after remastering. The HowTo says to remove it but I didn't have one.

Here is a portion of my log:

Code:
root@Microknoppix:/mnt/sda2/root/KNOPPIX# mkisofs -R -U -V "KNOPPIX.net filesystem" -publisher "KNOPPIX www.knoppix.net"
-hide-rr-moved -cache-inodes -no-bak -pad knx/source/KNOPPIX 
| nice -5 /usr/bin/create_compressed_fs - 65536 > knx/master/KNOPPIX/KNOPPIX 
Warning: creating filesystem that does not conform to ISO-9660.
2 processor core(s) detected
Warning, number as file string found. Assuming old command syntax and
choosing compatible parameters (-m -B 65536). See the usage info (-h)
for better/correct parameters.
Block size 65536, expected number of blocks: 2147483647
Ignoring file sm.bak
Ignoring file trusted.gpg~
Ignoring file mplayer.conf~
Using bt8xx000 for  ./.rr_moved/bt8xx (bt8xx)
<snip>
 99.87% done, estimate finish Thu Nov  4 11:45:23 2010
[ 9] Blk# 32500, [ratio/avg.  46%/ 38%], avg.speed: 2909816 b/s, ETA: 131416s
Total translation table size: 0
Total rockridge attributes bytes: 9654685
Total directory bytes: 28191440
Path table size(bytes): 141180
Max brk space used 47f4000
1041322 extents written (2033 MB)

Statistics:
gzip(0):     0 (    0%)
gzip(1):     0 (    0%)
gzip(2):     0 (    0%)
gzip(3):     0 (    0%)
gzip(4):     0 (    0%)
gzip(5):     0 (    0%)
gzip(6):     0 (    0%)
gzip(7):     0 (    0%)
gzip(8):     0 (    0%)
gzip(9): 32542 (1e+02%)
7zip:     0 (    0%)
Writing index for 32542 block(s)...
Writing compressed data...

root@Microknoppix:/mnt/sda2/root/KNOPPIX# ls -l knx/master/KNOPPIX/KNOPPIX 
-rw-r--r-- 1 root root 824974599 Nov  4 11:45 knx/master/KNOPPIX/KNOPPIX

root@Microknoppix:/mnt/sda2/root/KNOPPIX# md5sum /mnt-system/boot/isolinux/minirt.gz /mnt/sda2/root/KNOPPIX/knx/master/boot/isolinux/minirt.gz 
8dac243b731c1d32036874b31a2776ac  /mnt-system/boot/isolinux/minirt.gz
8dac243b731c1d32036874b31a2776ac  /mnt/sda2/root/KNOPPIX/knx/master/boot/isolinux/minirt.gz

root@Microknoppix:/mnt/sda2/root/KNOPPIX/knx# cd knx/master

root@Microknoppix:/mnt/sda2/root/KNOPPIX/knx/master# find -type f -not -name sha1sums -not -name boot.cat -not -name isolinux.bin -exec sha1sum '{}' \; > KNOPPIX/sha1sums 

root@Microknoppix:/mnt/sda2/root/KNOPPIX/knx/master# mkisofs -pad -l -r -J -v -V "KNOPPIX" -no-emul-boot -boot-load-size 4 -boot-info-table -b boot/isolinux/isolinux.bin -c boot/isolinux/boot.cat -hide-rr-moved -o /mnt/sda2/root/KNOPPIX/knoppix.iso /mnt/sda2/root/KNOPPIX/knx/master 
genisoimage 1.1.10 (Linux)
Scanning /mnt/sda2/root/KNOPPIX/knx/master
Scanning /mnt/sda2/root/KNOPPIX/knx/master/KNOPPIX
Scanning /mnt/sda2/root/KNOPPIX/knx/master/KNOPPIX/modules
Scanning /mnt/sda2/root/KNOPPIX/knx/master/boot
Scanning /mnt/sda2/root/KNOPPIX/knx/master/boot/isolinux
Excluded by match: /mnt/sda2/root/KNOPPIX/knx/master/boot/isolinux/boot.cat
Writing:   Initial Padblock                        Start Block 0
Done with: Initial Padblock                        Block(s)    16
<snip>
 99.68% done, estimate finish Thu Nov  4 12:00:33 2010
Total translation table size: 2048
Total rockridge attributes bytes: 3835
Total directory bytes: 10240
Path table size(bytes): 70
Done with: The File(s)                             Block(s)    406124
Writing:   Ending Padblock                         Start Block 406165
Done with: Ending Padblock                         Block(s)    150
Max brk space used 1b000
406315 extents written (793 MB)

root@Microknoppix:/mnt/sda2/root/KNOPPIX/knx/master# ls -l /mnt/sda2/root/KNOPPIX/knoppix.iso 
-rw-r--r-- 1 root root 832133120 Nov  4 12:00 /mnt/sda2/root/KNOPPIX/knoppix.iso
Booting the new image with QEMU results in a loop of error messages after the
KNOPPIX 6.2 splash screen:

Code:
 boot:
Could not find kernel image: knoppix
So the image is larger than I started with and I only added two packages and removed over a dozen.

Thanks,

Job