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It is usually a mix of our crawl timing and a quantity/quality trade-off. We try to filter out some low-quality links. Crawl timing has been faster recently, though (maybe 2 weeks), so generally that's only a short term issue. There are cases, though, where a link might not be crawled or counted - nofollow, bad headers, no crawl paths, etc. I've seen Yahoo Directory and DMOZ links, for example, that were buried so deep even Google didn't crawl them. Unfortunately, it's really tough to tell without seeing the site in question. If these are very recent links, then it's just an issue of time. If these links have been around for a month or more, then this could be a quality issue or a technical issue with the link.