Ø  I don't know if it effects MPSSE mode but you might check the latency timer. 
The latency timer tries to avoid partial data packets by waiting for more data 
to show up before transmitting. If you partially fill the buffer it waits for 
the timer (default is 16ms at least for FT232R) to expire before sending the 
packet.

You should be able to use ftdi_get_latency_timer() with a valid context and 
byte sized variable to get the timer in ms.

Is this related to the ftdi_set_latency_timer, in both of my examples I set it 
to 2

    status = ftdi_write_data_set_chunksize(fc, 512);
    status = ftdi_set_interface(fc, 0);
    status = ftdi_usb_reset(fc);
    status = ftdi_set_latency_timer(fc, 2);
    status = ftdi_setflowctrl(fc, SIO_RTS_CTS_HS);
    status = ftdi_set_bitmode(fc, 0, BITMODE_MPSSE);
    status = ftdi_usb_purge_buffers(fc);



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