I do seem to recall having to fix the Arduino library here for one of my projects: it had WAY too small of a serial RX buffer for my needs. Increased the buffer size, and problems went away.

Ahh.. here's the file:

arduino-x.x.x/hardware/arduino/avr/cores/arduino/USBAPI.h

Look for "#define SERIAL_BUFFER_SIZE" and make it bigger.