when did you respond to the first notice? paper filings can take 6 months or more before they are processed.
however, call your local office to see what they say. they can access your account (as can you online) and maybe tell you the status of your responses. they may require an in-person visit and request that you bring your proof. if that fails you should contact the IRS taxpayer advocate service in your state
https://www.taxpayeradvocate.irs.gov/get-help/roadmap/
by the way, was the payment mailed in, or did you use the IRS online service? if you mailed it, did it have your full name and address, tax year and SSN on it? I would think that this should be a simple matter that a local office can handle but you never know so start there.
