The Disbursement Report found in Blackbaud Merchant Services includes transactions processed online as well as transactions that were manually processed in the BBMS portal.
The Disbursement report is a canned reports whose options do not extend past the current available reporting options. Currently there is no way to distinguish between the kinds of transactions in the Disbursement Report.
In a Transaction Search within the Transactions section of BBMS, there is a field called 'Source' that defines if the transaction came in through a batch, card present, or card not present. This field also appears in the Daily Transactions report. Run a Transaction Search for the date range included in the appropriate Disbursement Cycle. These search results can then be exported from BBMS and compared those results of the Disbursement Report.