Revenue revenue total does not match Invoice total

We are running R12.1.3, with RPC2 applied against it.

A user has generated an invoice against a Project, with a Bill Through Date of 30/11/2015.

The Invoice Amount is 6,654.52.

They have tried generating the invoice using both of these jobs:

PRC: Generate Draft Invoices for a Range of Projects (PAIGEN)

PRC: Generate Draft Invoices for a Single Project (PAIGEN_SINGLE)

When they generate the Revenue with the same effective date, it generates a Revenue value of 9,234.52 (which is the total amount of all of the Expenditure Items raised against the Project so far).

They can't work out why the Invoice Amount is less than the Revenue amount.