That's what it is supposed to do. Once you hit "Save changes to drive", it saves the changes to the partition table (and thus there are no changes pending). You need to then reboot and format the partitions. They should show up as DH0:NDOS or DH0:Uninitialized (or something to that effect). Just click the drive and choose Format Disk from the Icons menu. (You only need to quick format).
