Complaint sub-issue: Trouble with how payments are being handled

I have been paying off my student loans to Discover aggressively over the last several months. In XX/XX/XXXX I had a total of {$6700.00} due. I paid off each loan sequentially until I had only {$780.00} remaining on a single loan this month ( XX/XX/XXXX ). I was paid on XX/XX/XXXX so I made my final payment the same day of {$780.00}. It was withdrawn from my bank account on XX/XX/XXXX. Oddly, there was no record of the payment on my online account. After approximately 5 business days I called to see why the payment had n't posted yet and was n't showing as pending on my account. The customer service representative told me they saw the payment but that it had been misapplied, but not to worry, they would reapply the payment and I would see it in 4-5 business days. I asked for something documenting this in writing. She told me that a letter would be sent to my home address. After the period of 5 business days and still no update to my online account I called again and was told the same information. I asked why it was taking so long to show up online and they said they were upgrading their computer system and it was taking on average 14 days for payments to be posted. My online account still showed a minimum monthly payment due of {$150.00} on XX/XX/XXXX which was due to be auto-deducted from my bank account so I again asked for documentation, in writing, that this payment had gone through so that I would not have to worry about additional payments. He agreed to remove the auto-payment but said he could not change what the computer said since they were going through an " upgrade ''. I e-mailed this week to ask for written documentation of the payment and received an e-mail back saying I still owed {$780.00}. I called and customer service now had " no record '' of my prior payment and said I could dispute that if I could show proof that the money had been withdrawn from my bank account. I asked why no one had asked for this proof before and was n't given an answer but I uploaded my bank statement through their " secure document center '' ( which will not let you see documents after they are uploaded, by the way ) and did not receive any further feedback. Today I received an e-mail stating that my " new '' minimum monthly payment is {$50.00} instead of {$150.00} and I have 13 payments remaining. I called and the customer service representative could see my dispute, but said it takes up to 90 days for it to be investigated. I, again, asked for written documentation of the dispute and was told that was not possible. That I would get a letter once the dispute was closed. I asked why I had gotten an e-mail with a new monthly payment when my loans should be paid in full and there is a dispute but was told that was automatically generated by the computer. I very much feel like I am being taken advantage of and they are refusing to close my account so they can continue to generate interest. 3 customer service representatives could supposedly see the payment and that it was misapplied, then now it 's missing and I need to file a dispute? No written record of any of this? I am fearful that I will be charged late fees, interest, and this will be reported to the credit agencies and I have nothing documenting any of these conversations.