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I would think that if a user wanted to reboot the computer, then logout and press CTRL-ALT-DEL for runlevel 3, if run level 4 then choose the option on the kdm menu. Either should initiate the shutdown process. If it is desired that the computer not reboot, then power off when BIOS screen is displayed.
Since FAT32 partitions do not have permission bits on the files or directories, I would think it would revert to the permissons of the mount point directory. Try changing the permisisons of that directory. (chmod 777 /mnt/hd) or whatever the name of the directory it is.
Maybe try to unmount the directory (as root), change permissions and then mount it again. Also check your /etc/fstab. It may be mounting it read-only.
An example line:
/dev/hda1 /mnt/win_c vfat user,exec,umask=0 0 0
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