I find here in my area, even with good agents, short sales can take extra time. If there is a second lender on the house then especially. Also, on a house that I just used as a comp, the sale contracted for $435,000 and the lender agreed and said they would pay the second lender $3,000. The second lender refused the $3,000. They went back and forth until the buyer, two months later, agreed to pay an additional $90,000 outside of the HUD-1 to the second lender. Whether you consider the price $435,000 which is what will be reported in tax data, or $525,000 is another debate, but one thing it does tell you is that a bank was willing to take $90,000 less then a buyer was willing to pay. Had it not been for the second lender the house would have sold way below market. That's what happens in most sale situations here.
Mostly, at least in most of my markets, I find that short sales sell in line with REO properties and REOs set the lower end of the value range due to the bank ownership stigma. For me, it has become a bank influenced stigma with short sales (where the bank must approve the price) included. I do have markets where all sales in the market are competitive with one another though.
Also, there are some short sales where the seller has the cash to make up the difference. On these short sales there should be no difference in price relative to the regular market, but then the agent does not typically advertise these properties as short sales.
My last thought is an agreement with the historical data problem and some appraisers overappraising the houses. I spoke to one appraiser, who was moving from my market because, according to her, they can't find work due to other appraisers making value while she appraises for market vaue, who told me she only uses sales that are not bank owned and are not short sales each and every time she does an appraisal. I'm sure she was responsible for a lot of over appraising on refinances and potential short sale properties, and she was probably surprised by all the good deals buyers were getting. When the market first starting going soft there was an agent and mortgage broker team team here who were taking the contracts and boosting their price to meet the inflated appraisal, thereby pocketing the extra cash for themselves. They were caught. But a house isn't worth more than what a typical person is willing to pay for it on the open market. Some appraisers, without knowing it, have been trained to make value. They just don't have a clue that they really do not know how to appraise, and now that the clients have gotten more strict on accurate values, they are losing work and not know why. (Not that there is all that much work out there to lose.)