A lender asks that you pay for appraisal to be sure they are not lending on an overpriced house. If it appraises for your price, they will move closer to committing on the loan. If it doesn't, they will ask that you provide more down payment. Once they have limited their risk as much as possible, they may commit.
Another good idea is to have the title searched for liens besides the one involved in the short sale.
A short sale can be a great bargain for the right buyer. You must be prepared to jump through many hoops and have plenty of patience. The process can take up to 5 or 6 months from start to finish. Usually in a short sale, the seller's lender will want an appraisal done to verify the market value in today's market. If the seller is not willing to pay for it, then you may have to incur that cost. My suggestion is to try to use the same appraiser that your mortgage company will use so you don't have to pay for a second appraisal. Once the market value is established the lender will determine if they are willing to accept your offer. If they accept your offer, then you're ready to move forward to closing if not, they may counter your offer or simply reject it all together.