Sounds like corrupt partition? maybe, maybe not, nonetheless a real real pain in the ass. However, merely botting of knoppix 4.01 and mounting then unmounting the drive (which is recognised by the BIOS and knoppix) then re-booting into ubuntu sorts it all out!?
why it happens? dunno…what i do know, its a pain in the ass to pull all them machines out just to get a CD drive in there to boot knoppix…