Get in to the details of FS10N and your custom report and find one line atleast that is present in one and not in another. Check for the characteristics of that line item and You will come to know why that difference is coming.
Actually you may compare the logic of Custom report with standard and that will resolve your issue.
Ex: Some of the document types are excluded or some user postings excluded or particular date based on which the report pulls the data and some thing like that.. are excluded like that
Regards,
Siva Cheruvu