I'm having issues with 2 things: Firstly, credit card payment with 2 banking matches, and second transactions that have been matched but never cleared.

Sure! Let me guide you on how to correct these two issues you encounter in QuickBooks Online (QBO).

First, when you make a credit card payment, it's logged as a negative entry in your bank account and a positive entry in your credit card account. This occurs because the payment decreases the amount owed on your credit card (positive entry), while simultaneously lowering your bank account balance (negative entry) to account for the payment made towards the credit card debt.

As a result, when you link your bank account and credit card in QBO, the transaction will appear as a debit in the bank account and a credit in the credit card.

You can match the downloaded negative and positive entries with the respective credit card payment you created. This will link to them together so you won't get duplicates. See screenshots below: 

It shows a negative bank account.

And positive to credit cards.

Also, about unreconciled transactions. Occasionally, you might find that transactions you have already reconciled reappear as unreconciled. This typically occurs when previously reconciled transactions are altered, prompting the system to classify them as unreconciled and bringing them back into the reconciliation process.

Let's verify the transaction status to ensure it is marked as reconciled. Please follow the manual reconciliation steps below:

1. Click the Gear icon and choose Chart of Accounts.
2. Locate the account you want to review.
3. From the Action column, click View Register.
4. Find the transactions. If the transaction is reconciled, you’ll see an “R” in the checkmark column.
5. If it doesn't, click the field to change the status. A Blank status means the entry is not cleared or reconciled.
6. Once done, hit Save.

It’s advisable to seek the guidance of an accountant before implementing this change. They will verify the accuracy of your financial records and ensure that your reconciliation balances are correct.

Also, I want to share a link you can use as a reference on how to run a bank report by cleared status in QuickBooks: Run a report of uncleared checks.

I'm present in this public space to assist you with reconciliation or managing transactions. Feel free to contact me by clicking the Reply button below.