Backing up from 1 External HD to another

[mdrdsr]

Scenario :

I have a MacBook Pro with 2 External FW 500GB (WD My Book Pro) Drives
Each EXT HD is formatted with 2 Partitions. One Partition is bootable and the other is just user files. I use SuperDuper to 1) copy all user files from the MacBook internal HD to EACH bootable partition on EACH EXT HD. My working files *live* on the 1st External HD. So, I 2) also copy, using my own SuperDuper script, all files from 2nd Partition on EXT HD #1 to the 2nd Partition on EXT HD #2.

This is what it looks like:
Bootable Clone Disk #1
User Files Disk #1
Bootable Clone Disk #2
User Files Disk #2


PS: The 2 EXT HD are daisy chained. Could there be some HD ID issues?


ISSUE:

Only the 2 bootable partitions are appearing in Finder or on Desktop. I have adjusted the Finder Preferences, deleted the pref Finder file. I *can* unmount and mount all 4 partitions via Disk Utility. Because I created an alias for each partition as well, I *can* access the partitions to work with data via these aliases. But it is inconvenient.

This happened the 1st time and I thought I messed it up so I reformatted both EXT HD and was back in business. This time I know I did not do anything inappropriate. I unmounted both drives. They spun down. I then disconnected the laptop and when I returned and plugged everything back, they will not appear in the Finder. I had successfully disconnected/connected several days prior to this.

QUESTION:

What is happening? Is it possible that copying from EXT HD Partition to the other EXT HD Partition is causing some kind of permission issues? I have verified and repaired all permissions on all disks -- no errors found.

Help? Thanks in advance,
David