Hello,
I think you forgot to "bless" the system folder on the second drive, or it is also possible that you had a SCSI ID conflict. How do you bless? After you copy the system folder to a new location (or build a new one!), you open it, and then close it, and ensure that the little system smiley is inside the folder icon on the new disk. This means that the Mac OS has recognized the folder as a valid system folder.
Glad it is working properly for you now though.
Christian
kc0arf
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