Missing Bytes reading FPGA data with FTDI 2232H

Here are my notes for the FTDI devices;

http://www.ovro.caltech.edu/~dwh/correlator/pdf/ftdi.pdf

and I've attached a loopback example program. There's one comment in there that may be relevant to your problem ...

    /* Set flow control per AN130 - apparantly this stops the
     * driver from dropping data.
     */
    ftStatus = FT_SetFlowControl(ftHandle, FT_FLOW_RTS_CTS, 0, 0);
    if (ftStatus != FT_OK) {
        printf("Error: FT_SetFlowControl returned %d\n", (int)ftStatus);
        return 1;
    }

Ah, but I see you already have that line in your code.

So perhaps your issue is with the interface logic. Look at the waveforms in the PDF I linked to. Use SignalTap II in your design to reproduce them. Perhaps you have an issue. Do you have a testbench that you have used to test your design?

Cheers,

Dave