I have had one, a Mega clone, running in a system for a month now and suddenly the USB part stopped working. I am not going to see it until tomorrow, so I do not know what the problem is, but I am worried. 100% or all of the boards have now broken, but of course that 100% means 1/one board.
The power supply is a common low drop regulator dropping from 8 volts. The whole thing is home made after the Mega R3.
I can tell it is broken because my customer has tested the system. Program is running as it should because output is correct but he/we cannot change the program. When I have time I'll try with the Atmel programmer.
I have now tested the card and it looks like the USB cpu is gone. It is a bit difficult to say of an smd device, but still. There is no change on the usb pins. Connectors and soldering is allright, allthough the shield of the usb cable could have oxidised. I cannot check the clock oscillator.
I think it is not quite proper to ask here about custom products, but the processor section is from Arduino Mega. So it is good to know if someone has had problems with Arduino Mega R3.
There has been a problem bricking the usb chip if you supply power to the +5v bus without disconnecting the +5v bus from the usb power bus. I do not know if that was your problem since you have a custom board.
This is the schematic for the Mega 2560 R3.
At the bottom of the schematic there is a T1 and IC7B. That is the isolation circuit. If Vin is higher than 6.6v, then T1 is disabled, and isolates the power buses. Does your board have the same circuit? If Vin is less than 6.6v, it does not isolate the buses, and has been known to damage the usb. http://arduino.cc/forum/index.php/topic,82046.0.html
SurferTim:
There has been a problem bricking the usb chip if you supply power to the +5v bus without disconnecting the +5v bus from the usb power bus. I do not know if that was your problem since you have a custom board.
I have noticed that our Mega board is a little picky about the order I connect the power and the usb cable. (But I thought all Arduinos are picky about this?) Is this a somekind of latch up problem. I think I'll cut the usb + power trace.
Edit: tried to make the meaning a little clearer in (But I thought all Arduinos are picky about this?).
I just looked through the ATmega16U2 datasheet. I could not find anything about the order which power supplies should be connected. Have to study some more.
Answer: Perhaps, if their power supplies are connected slightly wrong. I thought that power from the usb should be connected to UVCC. But it looks like that not now, UVCC should go to 5V.