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Fortunately, boot can be easily unset the same way you set it (using parted). But, when you do so, at least using the version of parted that comes with Ubuntu Gutsy, the msftres flag is set, and parted won't let you unset it no matter how many times you try. The main problem this caused for me was that the partitions marked as msftres would no longer be mounted automatically by OS X, so they didn't show up in the Finder, and they were grayed out in Disk Utility. diskutil list indeed showed their type as "Microsoft Reserved Data" or something to that effect. (I don't remember exactly, and I didn't feel like changing the type back just to do testing for this hint.)