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When I upgraded to 10.5.3, I noticed that spotlight was updating for ages ... I have two external HDs, one of them partitioned into two. I could hear them "chattering away" too, but more importantly, when spotlight is updating its metadata, you will see a spot in the middle of its "magnifying glass" on the menu. It took about 15 minutes, I think, to go through nearly 2 million files.

And yes, other apps were running more slowly while it did so.