From my experience, I strongly suspect that both the SS 1st and SS 2nd have a clause in their Short Sale approval letters that prohibits the Seller from receiving any cash. I will assume the Seller's agent is ethical and will not perjure him/or herself. The $3000, if paid, must go through Escrow and be shown on the HUD-1 as begin paid to one of the lien holders.
This kind of request for extra money usually comes because the 2nd lien holder is demanding that they be paid an additional $3000 or they won't agree to release the property and issue an approval letter. The Seller does not or cannot reach in their pocket to pay the $3000 , so they go to the Buyer and ask for more. Alternatively, they let it go in to foreclosure.
I would get further clarification from the Seller's Agent about the facts of this case sicne yu got a different explaination. Your Buyer's agent, if experienced in Short Sales, should be familiar with this problem. It happens all the time when a 2nd lien or HOA lien is in place. You can also seek legal advice from a short sale real estate attorney.
So, if the 2nd lien holder wants an extra $3000 and you agree, have the seller's agent give you a new HUD-1 showing what is proposed (who gets paid what). If you agree, you would draw up an addendum to increase the price $3000. Your lender will still require the home appraise.
Given the limited number of houses on the market, and my assumption the house is now worth more than your offer in this rising market, you might be best to bit the bullet if you can afford it. Otherwise you would need to cancel the contract and get your earnest money back.
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