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.