if the mega board hasn't been updated, they should use FTDI chip, arduino UNO is the only one using 82U
I'm guessing that the Mega2560 (my board) is pretty new them. It does have the 8U2 chip.
My board is the Mega2560, shown here: http://arduino.cc/en/Main/ArduinoBoardMega2560
I think you are referring to the Mega shown here: http://arduino.cc/en/Main/ArduinoBoardMega
maybe the HUB block some reset code or something similar used by avr-dude(the program that upload sketch)?
I don't believe that this is the case. When I attempt to upload through the hub, the LED on pin 13 flashes as usual to indicate a reboot. Even both RX and TX LEDs flash for a short time. I could attempt a manual reset at the appropriate time during upload to make sure, but the blinking LED I think means that its rebooted. (The sketch that was last uploaded makes use of an LCD display and doesn't touch pin 13.)
Do serial comunication works fine?
I can say with a certainty that the serial com works fine. Loopback works perfectly. Also, I have written a couple different sketches that rely on serial communications. I tested both by going through the hub after connecting direct to my computer for upload, and serial communications work fine with these sketches, no matter what route the data goes through.