Hello,
David Cuartielles from the Arduino Team here. I have been following this discussion trying to figure out what has been going on in this case.
Please note the following. We do not recommend connecting the Mega boards powering them from the 5V connector. Not the Uno R3 either. The voltage regulators we were using in the past (Arduino Serial, NG, Duemilanove, Diecimila, and part of the Uno's) would allow doing that. But the new way we use to bring power into the boards will not ensure the boards to work properly. That 5V pin is meant to be used to power sensors and low-current devices.
The fact that this issue is showing after a certain amount of hours of operation seems to be due to stress material. However I am just talking without scientific proof. Our hardware team is going to put some boards under test to check this point and see if there is a deterministic way to measure how long the boards run on this mode. I know this will not be of any help for your project as you seem to be interested in powering things from that 5v connector.
On the other hand, since our previous boards allowed this type of functionality, when documenting the new boards we copied material from the documentation files to the previous boards. There is one line about the 5v that says (and I quote textually):
5V. The regulated power supply used to power the microcontroller and other components on the board. This can come either from VIN via an on-board regulator, or be supplied by USB or another regulated 5V supply.
.. that last part should not be there:
or be supplied by USB or another regulated 5V supply
If you want to power up your boards you should be using the Power Jack, Vin, or the USB port.
This is obviously an error on our side and we will replace the original Arduino boards you got bricked. Please send me an email to: d.cuartielles AT arduino DOT cc with the serial numbers of the damaged boards and their models. Include your preferred shipping address. I will make sure the same boards are shipped to you the minute after I get that email.
I am sorry for the non-Arduino branded boards. As you know we don't support those.
Thanks for your understanding and thanks for helping us finding out this error in our documentation. We will fix that immediately.
/d