The last time I used the board I had connected to 5V external power at the same time as the USB - I'm not sure if that was a mistake and I've fried something.
If you applied the 5v to the 5v bus and the USB power at the same time, you could have fried the USB IC. This is from the Mega 2560 products page.
The board can be supplied with power either from the DC power jack (7 - 12V), the USB connector (5V), or the VIN pin of the board (7-12V). Supplying voltage via the 5V or 3.3V pins bypasses the regulator, and can damage your board. We don't advise it.
http://arduino.cc/en/Main/ArduinoBoardMega2560
Here is a thread that covers the failure.
http://forum.arduino.cc/index.php?topic=82046.0
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