Run HDToolbox again with both drives connected and click on the old 2.1 gig drive. If a requester appears telling that drives have been added or removed, let it save the changes. Reboot and check if the partitions are shown now.
If not, you should either make smaller partitions or increase the block size. Use the "Change" button in the "Partition drive" dialogue to change the file system block size. Do this for each partition which is not shown.
If you want to boot from the 40 gig drive, don't forget to set the "bootable" checkbox for the boot partition.
Bye,
Thomas
