In a short sale your offer is really made to the Seller and they have to accept your offer, which will be contingent upon what the Seller's bank will accept. If you really need to have your closing cost covered this should, ideally, have been in your original contract offer.
Once the seller accepts the contract it is submitted to the seller's lender. They will review the offer and Title/Escrow will prepare a HUD (closing statement) showing the Seller's lender how much fees and how much money the seller's lender is writing off. That lender then submits to the "powers that be" for approval. If they don't like what they see then then counter back to the Seller. Who counters back to you. When you make changes to the contract this upset's the flow and can put the file at the bottom of the stack and delay your approval.
Talk with your agent and lender so that you have a contract you can perform to.