The same issue with my Mega2560. Reproduced with IDE 1.0.1 and 1.0.4.
I'm disappointed. It seems Arduino is NOT so user-friendly as people say.
Too much headache for too much money... It is more convenient now to buy Raspberry Pi with ADC chip if needed.
Here is my boot log:
/home/user/bin/arduino-1.0.4/hardware/tools/avrdude -C/home/user/bin/arduino-1.0.4/hardware/tools/avrdude.conf -v -v -v -v -patmega2560 -cwiring -P/dev/ttyACM12 -b57600 -D -Uflash:w:/tmp/build7626980947593966222.tmp/TempMonDS18B20.cpp.hex:i
avrdude: Version 5.11, compiled on Sep 7 2011 at 19:34:16
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is "/home/user/bin/arduino-1.0.4/hardware/tools/avrdude.conf"
User configuration file is "/home/user/.avrduderc"
User configuration file does not exist or is not a regular file, skipping
Using Port : /dev/ttyACM12
Using Programmer : wiring
Overriding Baud Rate : 57600
avrdude: wiring_open(): releasing DTR/RTS
avrdude: wiring_open(): asserting DTR/RTS
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
avrdude done. Thank you.