The difference w/Bank Owned properties is they hire Asset Managers to do the negotiating for the bank; Short Sale properties do not, the bank will wait until they get the highest and best offer, that can take a while. So make your Short Sale offer your Highest and Best!
If you have a home that you want to put an offer in on and you really want the home it's going to be in your best interest to have your Realtor determine fair market value and base your offer on that and if there are any other offers on the home. If there are no other offers you can start out below the fair market value. Your Realtor will be able to determine fair market value from comparable homes that have recently sold in the area. Your Realtor can check with the Seller's Realtor to see if they have any other offers on the home and whether or not they're accepting multiple offers so you know how to present your offer. If you're dealing with a home that has multiple offers on it than "yes" you could be in a position of having to offer more than the list price. Just make sure that you're working with a Realtor who knows Short Sales - as this can be the difference between owning your new home or not.