I'm having the same issue (Leopard 10.5.1 and SuperDuper 2.1.4). I have an extra internal HD with two partitions: one for Time Machine, and one for SuperDuper. I have SD scheduled to clone my main internal drive every night.
I put both of these partitions in the "privacy" list in Spotlight to prevent indexing. However, every time I start up my computer, the SD clone partition no longer appears in the Spotlight privacy list, and Spotlight proceeds to start indexing it. I have to manually add it back to the privacy list to stop indexing.
The Time Machine partition always stays in the Spotlight privacy list, however.
I receive no errors during backups. However, at the end of the backup process, SD restores the Spotlight search indexing state on the clone partition, and I'm wondering if it's just not doing that correctly -- causing it to disappear from the Spotlight privacy list.
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