I was able to rent the home for $2600 but the lender is accepting the appraisers rental value of $2050.

In retrospect, I did not negotiate very well; I accepted their counter which was just below the list price.

Do I need a *business* checking account to accept rent payments and pay for maintenance/repair costs as they arise?

I've had a Craigslist rental ad up for weeks with no issues, no discriminatory verbiage, etc and since I had a "run in" with a local RE agent who was trying to force me to take her applicant (who was on every program in the book; not that there is anything wrong with that) I believe she is behind the flagging since I wouldn't accept the applicant.  

The payment has a clause: By accepting this payment, I acknowledge and accept the following terms:I am the property owner (or an authorized agent for the owner) of the above-referenced property and I am authorized to receive payments.

Due to market condition, I accepted an offer which is $20K below asking and additional $20k credits towards closing.

My profit on this sale is slightly less than the requested discount so I am not willing to accept it.

You can't say no to them if they ask if you accept it, but you can likely find a reason to reject their application.

Stop fighting it and start accepting it.

They sent a repair man the next morning, repaired the flame sensor... no charge and they would not even accept a tip.