When I get my comps, I only pull them off of the MLS. So a short sale that was basically agreed to by the lender would indeed affect the comps. Similarly I just represented a buyer and he bought an bank owned property for 70k under comps so that was on the MLS as well, (note the bank used a realtor) so in general as long as the home made it to the MLS it would indeed make it in the comps that at least most of us Realtors use. As for appraisers, I am not sure how many other sources besides the MLS that they use for the comps they generate.
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