What? The current Uno and mega board use the same USB serial converter chip.
This is only true if mega means Mega2560, the Arduino Mega (http://arduino.cc/en/Main/arduinoBoardMega
) uses an FTDI chip for the USB2Serial conversion and so uses a different driver than the UNO.
The OP wasn't clear about which one he uses, so if we take him literally zoomkat was right with his finding.
That is why I used the word 'current' in my statement. If you want to compare older boards then at one time the standard 328P based Duemilanove board and the then 1280P based mega board also used the same FTDI based USB serial chip. So trying to parse the statement:
The uno and the mega have different serial port hardware
To be other then a generally incorrect statement, and also with no bearing on what may or may not be the OP's problem is just an exercise in parsing for parsing sake.