Virtex-4 IBIS files generated by IBISWriter will omit any Low Capacitance differential inputs from the [Diff Pin] list. Low Capacitance inputs are assigned by way of the CAPACITANCE attribute (see the Virtex-4 User Guide for details).
This problem will be fixed in a future ISE design tools release.
The [Diff Pin] list can be manually annotated to include all differential inputs. For minimum differential voltage requirements, refer to the Virtex-4 DC and Switching Characteristics Data Sheet.