I've got the same problem using an arduino UNO with a atmega328p. Did you find any solution yet?
avrdude: Version 5.11, compiled on Sep 2 2011 at 19:38:36
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is "C:\Arduino\hardware\tools\avr\etc\avrdude.conf"
Using Port : \\.\COM6
Using Programmer : stk500v2
Overriding Baud Rate : 115200
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
AVR Part : ATMEGA32
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
eeprom 4 10 64 0 no 1024 4 0 9000 9000 0xff 0xff
flash 33 6 64 0 yes 32768 128 256 4500 4500 0xff 0xff
lfuse 0 0 0 0 no 1 0 0 2000 2000 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 2000 2000 0x00 0x00
lock 0 0 0 0 no 1 0 0 2000 2000 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
calibration 0 0 0 0 no 4 0 0 0 0 0x00 0x00
Programmer Type : STK500V2
Description : Atmel STK500 Version 2.x firmware
Programmer Model: Unknown
avrdude: stk500v2_ReceiveMessage(): timeout