Short Sale Negotiations --- am I being taken advantage of?

[Marisa Post]

Hi BP! 
I've been in the short sale process for about 6 months now on a home in Southern California. We're getting close to the finish and are now talking about closing costs, etc. with the listing agent / short sale negotiator. 

My main issue is a new "Transaction fee" that has been applied to my settlement costs to the tune of 1% of the purchase price. I've done my research and I know that this fee is perfectly legal, yadda yadda. The problem I have is in the disclosure of this fee. 

1) The listing agent says that the fee was in the MLS listing. However, I am being represented by my Father in Law who is a commercial RE agent. He does not participate in the MLS and I found the listing on a public site. I have never seen the fee mentioned anywhere.

2) The listing agent says that the fee has been included on every HUD we've received. The first HUD I received was in January 2015 (offered in November 2014, contract signed with seller November 2014). That HUD did NOT have this transaction fee listed. The first HUD I received that I saw such a fee was in March 2015.

To add to the shadiness of this fee situation, shortly after I brought up this "new" fee that was being added to the sale, the listing agent sent me an addendum to the "Residential Listing Agreement" which extends the listing until October 2015 and states the commission split and 1% transaction fee and has been signed by the seller. She has asked me to sign. I haven't signed because I feel like this is her way of going back to cover her *** for not properly disclosing this fee in the first place. 

BP, am I right to fight this fee? I'd be happy to answer any further questions y'all may have, but I am having a hard time with this as I feel like I'm being taken advantage of. Any advice?