This is perhaps due to the fact that the Knoppix kernel is not configured for Multi-LUN support. You could recompile and see if that fixes it.
I have two USB devices: a Seagate 20MB hard drive, and a CF Reader. When the Seagate is plugged in at boot, it hangs at the device configuration stage of the bootup. When the CF Reader is plugged in without the Seagate drive, bootup goes normally only when the reader is plugged into one of my two USB ports; when plugged into the other, it hangs during autoconfiguration just like the Seagate drive. (The Seagate drive behaves identically no matter which port it is plugged into.) I can boot using failsafe, but, of course, no usb devices are found.
How can I get more information about what is going wrong during the autoconfiguration process? In particular, the fact that the CF Reader works differently depending on which USB port it is plugged into suggests to me that this might be a bug. Any suggestions?
This is perhaps due to the fact that the Knoppix kernel is not configured for Multi-LUN support. You could recompile and see if that fixes it.
I don't understand what Multi-LUN has to do with it. The problems I have show themselves when only one USB device is plugged in. Am I missing something?

IBM System X3850-X5 Server w/4x Intel Xeon E7-4870 CPU , 512 GB DDR3 RAM,NO HDD
$1299.99
IBM QRadar xx29 2x Xeon E5-2650v4 2x 900W PSU M5120 12x 3.5" Bay Server No RAM
$179.99
Unused IBM 09P0037 MAINBOARD For RS/6000 7044-170 P-Series
$375.00
Rare Vintage IBM 93ZZ PowerPC Server Board - MCM Ceramic CPU - 40N1844 - 1.1 lbs
$49.99
IBM 02YC027 Seagate ST2400MM0129 2.4TB 10K SAS 12Gb/s 2.5" Server Hard Drive
$200.00
IBM SYSTEM X3500 M3 SERVER 7380AC1 TOWER Server XEON E5620 8GB RAID SEE NOTES
$110.30
IBM System x3550 M3 1U Server Intel Xeon E5630 4GB DDR3 No HDD
$279.99
IBM Power 8 S822L Server 8247-22L POWER8 Enterprise 256GB RAM 2x 00KV626 CPU
$999.99
IBM ADP Server Type 7870 AC1 NO HDD | 128GB RAM PC3L | 2 x Xeon E5620
$199.99
IBM Server Rackmount Sliding Rail Kit ( Part Numbers: 00D9375 / 00D9374 )
$24.99