When the report is run using selected funds, the report does not include the payments that are to a different fund other than the one being filtered on. When the report is run using all funds, the report does include the payments that are to a different fund (since gifts to all funds are being included).

To find the payments that cause this run the report in detail format (select Detail in the Report Type field on the General tab) for both all funds and selected funds. Study all of the payments listed for the fund(s)in question in each report to find the payments causing the discrepancy.