Hi, Barry.
If you reboot from the external drive, all the paths to the files on the internal drive (and the external drive, for that matter) change. Therefore, Spotlight reindexes the volume. This is both normal and necessary: while you can turn indexing off completely for the drive, you can't stop this behavior if you want to search with Spotlight.
We do allow you to disable indexing for the backup, though. There's a FAQ entry that provides a small script that will automatically do so -- take a look!
Hope that helps...
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--Dave Nanian
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