The 9.1i iMPACT software allows for indirect programing of SPI devices connected to a Virtex-5 device. When a blank check is run on the SPI device, the software generates conflicting error messages. The software pop-up display is not aligned with the report in the log window.
This problem has been fixed in the latest 9.1i Service Pack available at:
The first service pack containing the fix is 9.1i Service Pack 2.