Are you using SPI1 connector (A interface) or SPI2 connector (B interface) ?
There are two SPI connectors (pin headers) on the board: SPI1, which is
connected to the FT2232H's A interface, and SPI2, which is connected to the
chip's B interface. Both can be used to flash SPI chips:
flashrom -p ft2232_spi:type=tumpa,port=A
flashrom -p ft2232_spi:type=tumpa,port=B
The default interface is A, so for SPI1 you can also just write:
flashrom -p ft2232_spi:type=tumpa
I tested all operations on both interfaces, everything works fine.