What does your Realtor say? Hopefully you have a Buyer's Agent working for you. As others have said, it's hard to tell without seeing the contract, or being part of the transaction. What was the sales price of the home? If you asked the seller (B of A) to pay your closing costs, then this is their response to your request. It sounds like the total of agents' commissions AND closing costs cannot exceed $9K. It's very common for the bank to reduce the agents' commission amount on a short sale. They typically only offer a certain percentage of the sales price, and the agents have to split that 50/50.
As far as your comment about getting the best deal....guess what? You're going to get whatever the bank is offering. And you can either take it or leave it. It may or may not be "the best" deal. This is why I tell all my buyers that buying a short sale isn't always a great deal. The bank will only allow the sale if they are getting "fair market value" -- basically what other homes have been selling for in the area.
Again, hopefully you're being represented by an agent? He/she should be the one answering your questions. If not, sounds like Yve is willing to look at it for you, which is very generous.