I am having this problem also.   Intuit  Payroll is posting payroll to an old account.  It took a few months for me to realize this was happening but I resolved it by unreconciling back to the month, then going into AR and changing the bank from the old bank to the new bank.  I then went into reconciliation and deleted the transaction I put in there to help reconcile.  I don't need that now because AR will put the Payroll transaction into my reconciliation page. Then just reconcile as usual.  Continue to the next money.  You can do all the months that were in error at once but I prefer to do them one month at a time just to keep all straight.  Hope this works for you.  I'm in desktop Enterprise.