Sorry for constantly bothering you with issues ... but ...

In ft2232_spi_wr_and_rd() on a write the max_xfer is set to 4096:

This is used to limit the xfer value to something below max_xfer. Subsequently mpsse_store() is called and finally mpsse_write(). The return values of mpsse_write() is compared with xfer len+3:

The problem is that mpsse_store() will internally already call mpsse_write() whenever the buffer is full e.g. here:

Upon return mpsse_write() returns the number of bytes written. The problem is the previous comparison with xfer_len+3 will fail if mpsse_store() has already emptied the buffer and called mpsse_write itself. The final mpsse_write() will then only return the length of the last chunk.

This is triggered when writing to a full speed device with endpoints of 64 bytes. Data to flash seems to be written in chunks of 256 bytes which does fit into the 4096 bytes max_xfer limit but more importantly it also fits into the buffer of a high speed usb device with 512 bytes endpoint buffers. I am using a full speed device and thus this triggers.

This will also trigger if some upper layer tries to write > 512 bytes in a chunk. This just never seems to be the case.

May I suggest to just change