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Does this make any difference in Google? I mean a competitor site shows say 200 links while mine only shows 28 when in fact we have about the same # of incoming links coming from other sites.
Thanks, Dan
Google will spider both relative and absolute urls, so that shouldn't be the problem. Most of the time relative urls are better - they load faster and are easier to maintain/update with some html authoring tools (e.g. Dreamweaver in particular).
Could your problem be that a lot of your internal pages have dropped in PageRank, whereas maybe your competitor's haven't? Check the PageRank of the pages that are missing from the backlink count. Are they PR 3 or below? If so, then they won't show up. Generally pages need to be PR4 or better to show up in the backlinks.