Even if the mortgage balance is less, the total amount owed would have to add up to more than your offer, otherwise it wouldn't now be a short sale. There are probably late fees, penalties and now that they are delinquent in their payments most likely legal fees which could easily run several thousand dollars.
You certainly can submit a new offer on the short sale, but keep in mind it can take 2 - 6 months or even more to get a response from the seller's lender(s), and they can reject any and all offers, including full list price. Banks are not obligated to cooperate on a short sale. Make sure you are using a buyer's agent that has a good track record on short sales, one that can guide you through the process.