I feel for you.
We just had something similar happen. I have worked in real estate for years, but not active now. I have no short sale experience and have only sold condos and city houses - no big country/ suburban homes so we also decided to let the short sale 'expert' realtor represent us, with a very reduced referral fee. First of 7 purchases that I haven't represented us directly on... and of course it was a nightmare.
We are meant to close on our short sale tomorrow. I managed to get an early copy of the HUD and there is an $840 fee to the realtor's company to be paid by buyer (us) on top of the commission due from the seller/ short sale bank.
We had signed nothing saying we would pay any additional fees (there is no way I would agree to pay extra to anyone without knowing exactly what it was for), so I guess he thought he could sneak it in and we wouldn't notice?
I basically called the title company and said we were disputing the charge. Title company said to take it up with the realtor so I sent him a note on Friday copying in the title company saying that there had clearly been in error with the charge and could he remove it ASAP as we didn't want a mistake to hold up closing.
I guess the (albeit) mild threat of not closing worked, because I followed up a couple of hours later in another email copying in realtor and title co and the charge had been removed.
I loath things like this - it really is what gives all realtors a bad name.
When are you due to close? I wonder if it's worth telling him that you will be unable to close with the fee as it stands. The problem is that you signed an addendum saying you would pay all that extra cash. Over $3000 is a lot of money - where does the addendum say it is going? I think you are on shaky ground as he has it in writing that you will pay, but it depends on what the addendum says. How do you know it's to himself if it's under a different company name? Can you call the title co and have them explain to you what the charge is?
Good luck!
EDIT: I reread your OP - he said the company name was the title co and now the title co is saying it's not for them. Correct?
Then I would email a (business like, not angry) letter to both title company and the realtor stating that you were told additional charges were due the title company and that you will need a full accounting of where the $3200 is going before closing can take place and if it's for anything other than title charges as represented it will need to be removed.
Request the negotiator at the short sale bank's contact information in the same email.
I think it's your only chance. If you outright accuse them of fraud you will force them to take a stance and fight.
I too would want to nail them to the wall as to say a fee is for one thing and then it be for another is fraud. So sorry that this happened to you. I wouldn't have believed it, but the shady business practice I have witnessed these past few months have been astounding and now there is little that would surprise me!