Arduino mega 2560: atmega16u2 device signature fail

Development Tools IDE 1.x
1

Hello everyone, I've got a problem with my Mega2560 rev3
If i try to upload a sketch with the normal usb cable it fails every time, but using another arduino as ISP or even as serial with a manual reset it works.
I've tried to check the atmega16u2 with an Arduino as ISP and avrdude, trying also to reset the fuses values, but every time I get the following message:

icearrow@netbook:~$ avrdude -b 19200 -c avrisp -p usb162 -v -P /dev/ttyUSB0 -F -U lfuse:w:0xEF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0xCF:m -F

avrdude: Version 5.10, compiled on Mar 23 2010 at 15:03:00
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch

System wide configuration file is "/etc/avrdude.conf"
User configuration file is "/home/icearrow/.avrduderc"
User configuration file does not exist or is not a regular file, skipping

Using Port : /dev/ttyUSB0
Using Programmer : avrisp
Overriding Baud Rate : 19200
AVR Part : AT90USB162
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC6
RESET disposition : possible i/o
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 65 20 4 0 no 512 4 128 9000 9000 0x00 0x00
flash 65 6 128 0 yes 16384 128 128 4500 4500 0x00 0x00
lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00

Programmer Type : STK500
Description : Atmel AVR ISP
Hardware Version: 2
Firmware Version: 1.18
Topcard : Unknown
Vtarget : 0.0 V
Varef : 0.0 V
Oscillator : Off
SCK period : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.06s

avrdude: Device signature = 0xffffff
avrdude: Yikes! Invalid device signature.
avrdude: Expected signature for AT90USB162 is 1E 94 82
avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as FF
avrdude: safemode: efuse reads as FF
avrdude: reading input file "0xEF"
avrdude: writing lfuse (1 bytes):

Writing | | 0% 0.00s ***failed;
Writing | ################################################## | 100% 0.16s

avrdude: 1 bytes of lfuse written
avrdude: verifying lfuse memory against 0xEF:
avrdude: load data lfuse data from input file 0xEF:
avrdude: input file 0xEF contains 1 bytes
avrdude: reading on-chip lfuse data:

Reading | ################################################## | 100% 0.02s

avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x0000
0xef != 0xff
avrdude: verification error; content mismatch

avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as FF
avrdude: safemode: efuse reads as FF
avrdude: safemode: lfuse changed! Was ef, and is now ff
Would you like this fuse to be changed back? [y/n]
icearrow@netbook:~$

and if I press Y at the question it hangs until i terminate the program.

If I check the atmega2560 everything seems OK, with the right device signature.

What can I do?

2

Looks to me like the errors you would get if the Arduino running ArduinoISP got reset and you were talking to the Arduino bootloader instead of ArduinoISP. Did you disable the Auto Reset on the Arduino?

3

yes, I've put a 0,1 uF between RESET and GND as I explained in many guides.
As I said before, if I connect the ISP to the Mega2560 ICSP headers everything seems to be ok.
connecting to the 16U2 ICSP headers brings me the error.