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I've also noticed weirdness in doing normal searches, but I haven't been able to nail down a pattern yet.
Anyone else noticing strange behavior in the dupe filter?
3-5 pages, with the all-famous "some of your search results have been omitted..."
Yes, if the pages on your site are very similar to each other, it'll do that. For example, I have a site with 8 pages and a large amount of identical text on each page, and Google only returns 2 pages at a time.
It could be that the similar content filter has become more sensitive.