Make a new NTFS partition. Copy all files to the new partition to a FAT partition on Linux. Mount the drive containing the FAT partition on Windows and copy everything to the new NTFS one. Remove the old one and the FAT.

Another chance: there is a tool called "partition image" (http://www.partimage.org/) on Linux that allows archival and duplication of partitions including NTFS. I had no luck when I used it (WinXP still failed to read the original and recreated partition) but your mileage may vary. My Windows XP failed to read my old Win2k NTFS partition in the same situation as you are, but I just moved all the files needed to keep to my FAT partition and removed the partition altogether.

A Win2k install won't read a Win2k partition. That's strange. But it didn't come to me as unexpected as I haven't found NTFS reliable after all.