You've asked a great question, and the answer in your particular case is that your responsibilities with respect to compensating your agent should be clearly spelled out in your buyer's brokerage agreement.
It is a relatively (and unfortunately) rare practice in the City of Chicago to have buyers sign a buyer's brokerage agreement, but it is a practice that should be commonplace for the protection of both consumers like yourself and buyer's agents. Your agent should be applauded for having had you complete such an agreement.
Your agent should also be admonished for having not explained the consequences and duties of the agreement to you in a way that you fully understood.
Cathi Weaver's answer to this question I assume is based on either limited experience with such agreements or her reliance on "past or common practice" in Illinois and the City of Chicago, but she is simply wrong on this.
Blaison Samuel's answer is also quite off the mark. When a bank or lender is not being paid the full amount that they are owed on a mortgage, they are often very reluctant to pay "traditional" or full fees to other practitioners in a given transaction. Banks tend to ask the proverbial question- If I (the bank/lender) am being shorted, then why should everyone else be paid in full?
Virtually every short sale or foreclosure that I have been involved in has featured a re-evaluation of the realty brokerage commissions being paid at some point after the contract is agreed to but prior to (or at) the closing. the only times this does not happen are in cases where the bank has agreed to either a set amount or a set percentage of purchase price in writing in advance of the listing (and the cooperating commission being paid to buyer's agents) being posted on the Multiple Listing Service. Even in some of these cases the bank will want to make changes to commission agreements (i.e. when both the buyer and seller are being represented by the same Realtor).
I disagree with Gilda Baxter's statements about when a buyer's brokerage agreement is signed/used. Most (if not all) Realtors work on both the buyer's side and the listing/seller's side of transactions eventually. Even if the agent in question "specializes" in representing buyers or sellers, the need to have a written agreement in place with you that clarifies "each parties' rights and responsibilities, and also to spell out the minimum services required to be provided by Illinois law" (to quote Jeff Kropp's post) still exists in all transactions involving a buyer.
If in your case the amount or percentage that you've agreed to pay your agent is less than the amount that is being offered by the bank/lender or seller in the short sale transaction, then you should probably amend your original buyer's brokerage agreement with your agent. If you feel that you would like to make up the difference between the amount that your buyer's agent was expecting to be paid and what they're being offered on the short sale, then you could always "add" that difference to the amount that you would compensate that same agent (based on your intentions as stated in your original post to use them to also sell your current house) to the listing agreement that you sign with that agent.
You should be able to do either, but I would strongly advise you to get whatever agreement is finally reached (especially if you amend the original compensation from the buyer's brokerage agreement) in writing. And make sure that all of the relevant parties are notified. If you're not sure who the relevant parties are in the transaction, then ask your attorney whom should be notified of changes to compensation.
Without having known that you did already have an agreement in place with your buyer's agent, Thomas McCarey offered a pretty complete and thorough answer. I hope that my answer makes sense to you, but if it does not please feel free to contact me directly to clarify anything I've written here.
And to any Realtors reading this post, I'd strongly encourage you to not follow the "common practice" in Illinois and Chicago but instead have signed buyer's brokerage agreements with your buyer clients. You'll eventually save everyone a lot of confusion (and you'll protect your ability to get compensated at the same time).
Broker Associate, Sudler Sotheby's International Realty
1634 E. 53rd St. 2nd Floor Chicago, IL 60615
773-418-0640 (cell) email@example.com