OK You have applied the patched bootloader with SPI/i2C fix + changed the device-tree + kernel 4.9, correct ?
What appends if you reduce the frequency, does it still running at 400KHz?
Yes. I tried setting it to 1 and 3.4 MHz.
I'll try 1MHz one more time after applying the bootloader patch but with 3.4MHz, it's the same result.
What kind of I2C driver are you running, kernel or userspace one ?
Thanks a lot!