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I have used partition magic on a number of computers and haven't experienced the problem that you have written about. In fact, once you have installed an OS on a partition, whether it has been created by fdisk (Windows or Linux) or partition magic, this really shouldn't have any effect on how the OS operates.

Actually, there was a bug in PM at one point that created partitions with the wrong FS type in the partition table. This was a canned answer at RHAT at the time I worked there (2 years ago) but I do not know if PM has since fixed said bug. PM has also been known (in the past) to trash partition tables to the point of no return with any OS (winnt/linux/dos). Again, this was in the past and I have used to most recent version (PM6) without any problems to migrate a win2k/win98 system from one machine to another without any problems. As PM themselves say, make sure you have a backup of all your important data before using their product.