OK, so the wierdness continues.
A.) ldots, if you're still reading this, I have a bug report/incompatibility to alert you to -- it might be out of your hands, but hey, doesn't hurt to try. I have an Asus P4P800 Deluxe, which means the usual 2 IDE channels plus two SATA hookups. To get them all running, you use "Enhanced Mode". Windows XP speaks this just fine, but apparently iso-linux not so much. When I had it on, it kept getting confused and trying to disable a certain IRQ -- at first it was 11; I disabled that and it started on IRQ 5. Rather than play fingers-in-the-dam, I thought it might be all those ide devices. I was right. I turned it back to "Compatibility Mode" (no SATA) and it was fine. So, might at least be worth a 2-line note at the end of the readme.
B.) I've got a pretty good picture of the problem. ConfigMagic dumps the same BIOS file (AFAIK -- don't have a binary version of diff handy to test for sure but it prints identical in wordpad) as Evox, and when I load either eeprom file in liveinfo, it makes the right key. That is, the liveinfo-generated key matches the hddinfo.txt and eeprombackup.txt files. The linux tools (xinfo, etc) appear to read the eeprom.bin file incorrectly. The listed Unique HDD Key (which, as I understand, is from the EEPROM, not the hard drive, and thus a bit of a misnomer) matches the text files in windows, but is completely different in Linux. No idea where it's getting the values from.
I am unsure how to proceed -- I'm considering locking by hand, generating the new key here in Windows then locking in DOS, but I'm a bit scared because I don't own a working floppy drive to save logs with. If only the DOS utils had FTP support... I'll try to figure something out...