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I recently suffered through a painfully frustrating reinstallation of both windows 2000 and linux (I'm trying ubuntu right now). I installed a DVD-RW drive in my old slot-1 p3 box, and I guess windows just freaked out.
Anyway, I used knoppix to set up the new partition for windows (fat32), then installed w2k on the partition. On reboot, I got "Missing operating system". After hours of fruitless troubleshooting (also losing my linux installation too in the process), I finally tried my western digital "data lifeguard" tools floppy disk, which said that the partition information didn't match the boot sector information. And I noticed that knoppix fdisk didn't detect the lba geometry on my drives (hence losing my linux installation by monkeying around with partitions and using the wrong geometry). I finally fixed my disks by using ranish partition manager to delete the partitions and make new ones.
So, just a warning: if you use knoppix for any low-level disk operations, make sure it's using the correct geometry.
Which version of Knoppix were you using? There were problems about 6 moths ago related to the 2.6 kernel reading partition information differently than before, so problems occurred. It should only happen if you use certain distros (Mandrake 10.0, Suse 9.1, Fedora 2, others?) and modify the partition table (e.g., create new partitions to put Linux on).
It *should* be all straightened out in more recent versions. (Knoppix 3.7 is okay. )
Well that explains it then! I was using 3.6 and I usually booted it with the 2.6 kernel. I didn't realize 3.7 was out. Cool! Thanks for the update! In answer to the second question, it not only didn't read partitions correctly, it also didn't create them correctly. In addition to windows I was using gentoo, but now I've installed ubuntu because I don't have the heart or patience to reinstall gentoo.... (it only took a week, and then a few more weeks to get it configured correctly )