I thought of that too, but when I modified the 128 byte receive buffer in wiring_serial.c to be 256 bytes, I had the same problem. I want to stream at nearly full 115200 baud rates, but for this test I'm only just sending a block of 256 bytes at 1-second intervals - not even full bandwidth consuming rates, yet I still see this error.
It's more like new bytes are coming in during the interrupt from the previous received byte or something.