If any of the links are in heavy JavaScript then PhpDig won't follow them. Try setting a larger search depth, use links per of zero, and the no option. You can increase search depth beyond twenty by changing SPIDER_MAX_LIMIT in the config file. Also, if there are any META revisit after HTML tags, PhpDig attempts to obey those times. Tip: start indexing the site from the sitemap if present and check out this thread.
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