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Just a few possibilities out of many: Some links got lost. Or more links are being counted than we're seeing. Or some links that were counted before aren't counting for anything any more, and there could be any number of reasons for that.
I'm inclined to suspect the latter as a viable possibility. Possibly it's something to do with number of links from the same sites vs. number from different sites - it kind of looks that way in a couple of cases. Or something to do with the number of occurrences of the identical anchor text - which was becoming almost an epidemic well beyond SEO circles. Mom 'n Pops who just barely learned how to point a mouse were buying up and pointing multiple keyword-laden domain names to their websites because they read about it in some column someplace.
That part is a concern because in some cases the anchor text may be part of an established company name or site name, or part of it, for very legitimate reasons that have nothing to do with search engine placement.
Personally, based on my experience, I think that the links are counted but not shown.
"Personally, based on my experience, I think that the links are counted but not shown."
I would state it as;
I think some of the lost links / data / calculations are counted, but are not shown.
I am "fortunate" (from an analysis stand point) as sites I had been working on (in terms of getting back links, etc.) from around November last year to around May of this, have slowly and respectively made come backs. So I have the earliest of these sites now back as #1 to #3, and the later ones steadily rising as more and more back links get factored in.
I am 100% certain it is data, or rather calculation catch up, as I had two sites storming pre-dominic, then crash (oh look, no back links), and now coming way back uop again.
So many theories have been floated around and most have just been misinformation (although one or two snippets have been b useful). I still stay keep to what you were doing pretty much pre-Dominic and the smile will come back to your face soon enough.
Not immediately ;-)
Why do you think there are sites out there that you can not fathom why on earth they are ranking so well with so few back links?
I see the issues like this;
1) March(ish) Google finish their new algo and need to test it with real data. So they grab the data (which includes calculations for PR / relevancy) that is and run their tests.
2) April, while they are doing this, the old algo carries on, with new data being added, etc.
3) May, Google finish testing their new algo and launch it with the old data. They have to do this as they are certain of the results yielded and need to slowly watch what happens as the algo plays data catch up. Sites that were doing well, suddenly drop, and weird things a happen about index pages as Google algo's try to play catch up with proportioning internal PR as well.
4) New algo has new super, duper freshbot, that brings new stuff in quicker, and confuses the hell out of everyone because earlier data missing.
5) Freshbot working good now (although very Spammy to say the least). Regularbot data slowly catching up.
6) Backlinks and PR not showing as they should because process is a) collect data, b) calculate it, c) apply it, d) report it.