dlinear:
I think the problem is with the driver on the PC. I'm attaching waveforms I collected from the Arduino (pins 1 and 2) showing the data being sent/received and I can see signals on the USB lines (differential and occurring much much faster). But I still can't receive data (can send).I can use the "devcon" command from Microsoft to reset the Arduino USB port from the command line, and this resets the serial communication. I have to waive the white flag and use this hack as a solution, but this is hardly solved.
Could you detail what you're doing with the devcon command? I think I've been having this same issue and haven't found anyway to fix it. Is it a disable/enable command on the arduino.? Maybe you can just post the code that you run? Thank you for your help.