Donations that come in via ADF do not auto reconcile when a BBMS report automatically uploads to CRM. The do auto reconcile when they come in via a a standard donation form part, and also reconcile when they originate from CRM itself, such as in a ERB.
Download and install the latest Service Pack which contains all fixes from previous patches. If you are running an older version, download and install the latest version and then the patch.
Steps to Duplicate
Submit donation from Advanced Donation Form
Download and commit batch
Confirm revenue record is created
Run reconciliation process and note that transaction from step 3 is reported as missing