Confirm when you're Reconciling that you've put in the Statement Closing Date, not just letting QBs default to the current date.  Then if the Closing Balance is also per the Statement and you've got all the correct transactions checked off, the Reconciliation Balance should be $0/Balanced. 

All of the transactions prior to the Statement Date that have not cleared the Bank should not be checked.  Also any transactions that happened after the Statement Date should also not be checked.  There should also be a little Check Box (it's at the top on QB Desktop) where you can "Hide transactions after the statement's end date."  That should hide all of the newer transactions you're seeing.