I have also been having this issue for several months. QB will auto match credit card payments to the transactions and then automatically create a deposit. It is auto-matching e-check payments to transactions, but doesn't create the deposit. They sit in Make Deposits until I manually create the deposit.
This creates two separate deposits in QB, which don't match to actual bank transactions. I'm on with support now trying to get a better answer. I'm extremely dissatisfied with the payments solution at this point. The fees are higher and it's creating more work.
