Google doesn't show all backlinks in any of the tools available. It's "proprietary" information. There are more out there, they just won't tell you which and where.
The truth is that MSN and Yahoo probably don't show all of them either, but they tend to show a larger percentage.
If you want an idea of true link power, do what you've already done: total them up, then multiply by some factor.
I'd use something like this:
((MSN links x .5 per year of domain age) + (Yahoo links x .05 per year of domain age) + (Google links x 2.5 per year of domain age) / (count(spam links/spamlinks per day per IP cluster)-high impact links)) * weighted margin of error(where margin = .01*estimated number of Unicorns with natural tiger stripe fur)+(.5*num_genuine_hobbit_movie_swords_in_Matt_Cutts_Collection)
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