What law have they violated? The Fair Housing Act? Equal Credit Opportunity Act? Are you being discriminated against because of your race, color, national origin, religion, sex, familial status or handicap (disability)?
Let me know which one of these you believe the lender has violated: http://www.federalreserve.gov/boarddocs/supmanual/cch/fair_lend_over.pdf
You can read about Fair Lending Laws & their enforcement in this publication by the Federal Reserve Bank of Richmond http://www.rdmesq.com/downloads/CH_20_-_FAIR_LENDING_LAW.pdf
From what you said, it doesn't sound like the lender has violated any Fair Lending Laws. It does, however, sound like they have a bunch of monkeys in their back office (no offense to anyone who has a monkey, or monkeys themselves), which to my knowledge doesn't violate anything (except for perhaps local laws on keeping wildlife in a place of business, if indeed they do have monkeys working for them). However you should conduct your own audit on them - as it sounds like you know exactly what should have happened, so you should be able to give them a call and find out why they think what they think... and you can tell them what they think is incorrect, and provide proof of it. Right?
It also sounds like you have an approved modification. What are you looking to get out of what you'd be planning on doing?
http://portal.hud.gov/hudportal/HUD?src=/program_offices/housing/ramh/res/rightsmtgesrvcr & http://www.ftc.gov/bcp/edu/pubs/consumer/homes/rea10.shtm explains "Your Rights and the Responsibilities of the Mortgage Servicer" when it comes to handling payments, escrow accounts, etc. You can even write them what is called a "qualified written request under Section 6 of RESPA" which, by law, they must respond within 60 business days.
It states under Posting of Payments:
'The servicer must credit a payment to your loan account as of the day it is received. Some consumers have complained that theyâ€™ve been charged late fees, even when they know they made their payments on time. To help protect yourself, keep detailed records of what youâ€™ve paid, including billing statements, canceled checks or bank account statements. You also may be able to check your account history online. If you have a dispute, continue to make your mortgage payments, but notify the servicer in writing (see Sample Complaint Letter) and keep a copy of your letter and any enclosures for your records. Send your correspondence by certified mail to the address specified by the servicer, and request a return receipt. You also may wish to fax or email your letter and any enclosures. Be sure to follow any instructions the servicer has provided and confirm the fax number or email address before sending your letter. Keep a copy of transmittal confirmations, receipt acknowledgments and email replies."