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I have had a few funky repartitioning sessions myself. The last one was just a month or so ago. I was trying to repartition and format a laptop that had a linux distro on it to fat 32 so I could reinstall the original Win98se that came with it. Tried my Mandriva 2006 cd1 to do the job, would not, tried fdisk in dos, no go, tried Slack cd1, no go, tried Mandrake 8.1 cd1,worked! I have no understanding why, nearly flung it off the balcony! I know it is nothing to do with linux formatting because I had a similar experience with a desktop that had Win98se on it. A company that I worked at previously gave its union a pc with all admin rights locked out, and it was to be connected to the company intranet, they wanted it redone by a union member due to security fears. I started out trying to partition and format with dos, Mandrake, then it was a Slack disk that finally worked. Other than those two times I have never had any glitches repartitioning and formatting. Strange, I know. Luckily my persistance outweighs my knowledge.
I can only suggest try out a few different disks to see if that helps.
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