I fried an Arduino (Leonardo) in that same area, the area around the connector gets/got very hot. In my case I was asking for a bit too much from the 5V supply output to power an LCD with backlight. Even with only 8Volts input she burned right up. I find it interesting (annoying actually) that there is no specification from Arduino on the max current you can use for the 5V output, only the 3.3. Apparently it's not a lot. Also I would think that there was a overcurrent/temp limiter in there somewhere, but my $30 lesson is I guess not.
So if all else fails, consider that the input voltage may not be the problem, but the demand from the power circuit could be frying your electronics. So if you are using any 5V, do yourself a favor and get a nice, tough 7805 in a TO-220 package and don't rely on the Arduino to supply any juice.