Hi I am having similar difficulties with my Uno. It was working OK until I decided to use an external power supply. The guide suggests anything up to 12V is all right. I connected via a shield to the Vin pin. Everything seemed to be working OK for a while and then it all stopped - power light went out. Close inspection of the Uno schematics shows that the Vin pin is downstream of the 1N4007 diode that prevents reverse polarity mistakes. The diode also introduces a 0.7V (approx) drop. Found this out after I hooked up a 9V supply via the power in socket. Other responses suggest that an overvoltage power supply seems to cause problems. Since then I have tried the following. 1 Replace the ATMega328 chip - the new one must come with "Blink" preloaded because it blinks at me when powered up - but try to upload a new sketch and I get the familiar: avrdude: stk500_getsync(): not in sync: resp=0x00 avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x51 This seems to be a timeout response because it takes some time to appear - much longer than a normal upload.
2 Put the old chip back on board - and tried the "Loop Test" - it worked perfectly so serial communication via the USB is OK Without knowing what it could be - it seems that the board has been damaged and so prevents uploading from completing its course. Not sure what to do next except buy another one.