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OK, I did as you suggested. First I cleared out my tables, set the "links-per" and search depth as you suggested, then re-spidered my site. It might be looking for the proverbial needle in the haystack to find the differences between 1.8.0 and 1.8.1, but I'm still a bit short of the pages that should have been indexed.
1.8.0 - 1,514 pages
1.8.1 - 1,262 pages
If it would help, I can nose around and find some pages that weren't picked up by 1.8.1.
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