If you are concerned that your agent will not get paid for services rendered, he or she should (would) make you aware of lack of compensation on a property offered for sale and, prior to viewing and making an offer, would explain their policy for dealing with such a situation.
More likely than not, you would be responsible for compensation and your offer would reflecting that additional cost incured by you, the BUYER.
All it means is: if the purchase price is $300,000, and you get the seller to give you a concession of $25,000, that the Realtor will only receive commission on $275,000.
Very simple, and clear. I'm sure your agent understood it.
It's also our office policy that the commission is not paid on Seller Concessions. Many of the 1st time buyer programs that are available (FHA, etc) allows for a certain percentage of Seller-paid contributions (to be applied toward down payment, closing costs, prepaids, points, etc) 3% of purchase price seems to be the most commonly asked for contribution. Since the Seller doesn't actually net the sale price (minus concession) it's only right and correct that they not have to pay commission on that amount.
I just want to point out one thing (a technicality, but still you should be aware). If you don't have a contract, you don't have an agent working for you. Your agent may be working as a non-agent (without a contract) but legally, without a buyer agency agreement in place (which would also spell out all the terms of the agreement, including compensation, you do NOT have an agent. Look carefully at all of the paperwork that you may or may not have signed. Agency law is unfortunately not understood by the majority of buyers (and sellers to a lesser degree) and some agents as well.
I wish you all the best with the short sale. They require the patience of a saint (just waiting for a response can be a long wait) but you may be able to get a very good deal on a suitable property. Good luck :)
As far as your agents commission, if the property was found through the multiple listing service then they were probably offering compensation. If it wasn't then your agent probably submitted a request for compensation to the seller, then he would make sure to get paid. Hope this helps