Hello JonDen
I'm so glad to see that I'm not the only one facing this issue ! when i read to verify the value of the internal registers the last bit of data is always "0".
For example, I'm writing 0xFF to the IOConfig register but when i read the value its 0xFE or writing to the same register 0X01 reading 0x00.
To verify that the problem is in the read function and not the write function i set GPIO0 to low-> high-> low and i can see it changes.
Using:
FTDI: FT4232HL
SPI mode:3
Clock frequency:100Khz
Did you buy any change managed to solve this ?