I have had similar problems with Fannie Mae and Freddie Mac. I would have my agent get as much information from the listing agent as possible. I am sure the owner and listing agent want to sell the home as much as you want to buy it. It's very difficult these days to "low ball" a short sale, they banks in some areas are just not discounting them any longer.
I will say this, the fact that they countered with full list price is a pretty good indication they thought your offer was very low. Do your due diligence, look at recent sales of similar homes, factor in any repair costs and make your counter offer accordingly. A reasonable discount will probably be accepted but if you are too greedy, yes, they will lose the house. My buyers did and in my opinion THEIR offer was very reasonable.