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Backlash Against Mark-to-Market Accounting

I was wondering if you or some of your readers can you answer this for me: When holders of mortgage-backed securities write down the value of these securities, do they based it on: (i) the “fair value” of the MBS as determined by the rating agencies; or (ii) the collective market value of the underlying collateral as determined by independent third-party appraisals? I am finding it very hard to understand why the write downs in the value of these mortgage-backed securities as reported in various publications, do not seem to correspond to the drop in the value of the underlying collaterals.