On the Uno, and the mega2560, serial comms is handled by a atmel 8u2, not the less versatile FTDI chip used on earlier Arduini
There is a known bug in the previous firmware, whereby sketches that use Serial comms can prevent successful upload of new sketches
See the thread in the hardware section - you need to reflash the 8u2, and then report back if it's still broken. (Good news - you need the dfu-programmer software and 2 short pieces of wire - no new hardware to flash the 8u2!)
http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1286088093/0Good luck