When you compare the downloaded transactions in Quicken to those on the BoA website, is there anything special about those that were not downloaded? Are they the newest ones for example, or are they listed as pending?
I have found that if I download in the evening, the Online Balance downloaded from BoA includes transactions that are pending and will not download until the next morning. This causes the automatic reconciliation to fail. If I click on Finish later on the Reconcile screen, the reconciliation goes OK the next morning.
Does this match what you are seeing?
What method are you using to download the transactions from BoA? Do you do it manually from the BoA website, or do you use Quicken to initiate the download using One Step Update (OSU) or Update Now?
I am using OSU.