Sync issue, 13 not blinking, 2 arduino's deads ?!

Using Arduino Installation & Troubleshooting
#1

Sorry if I'm a bit direct bit I've for the moment 60€ of hardware not working anymore that really... :0...

So, it's apparently a known issue :

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:\Program Files (x86)\Arduino\hardware/tools/avr/etc/avrdude.conf"

Using Port : \.\COM3
Using Programmer : arduino
Overriding Baud Rate : 115200
avrdude: Send: 0 [30] [20]
avrdude: Send: 0 [30] [20]
avrdude: Send: 0 [30] [20]
avrdude: Recv:
avrdude: stk500_getsync(): not in sync: resp=0x00

avrdude done. Thank you.

The arduino is correctly recognized by the computer. The drivers are ok too. The com port is ok.

Without any solution, I've swapped the atmega328 from another arduino with faulty one. Before that I've just uploaded the blink 13 code to the working one, no problem. Once the new chip is on the faulty one I now have the same issue on both arduino bords. 13 is not blinking 3 times at the begining, just stays always high, and they can't be programmed.

I've try once again with one pre-bootloaded atmega328, same issue.

Any ideas ?

EDIT :
Also, RX blink three times when programmed (correspond to the three sends). And when I use a serial terminal to send data to the arduino, RX is blinking too.

EDIT2 :
I've try to reburn the bootloader, nothing changed

EDIT3 :
A preicison, the pin13 L is not bright, looks like dimmed.
Also I've actually configured my last uno as an ISP. When I try to upload the code to my faulty arduino I get :

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:\Program Files (x86)\Arduino\hardware/tools/avr/etc/avrdude.conf"

Using Port : \.\COM5
Using Programmer : stk500v1
Overriding Baud Rate : 19200
avrdude: Send: 0 [30] [20]
avrdude: Send: 0 [30] [20]
avrdude: Send: 0 [30] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
AVR Part : ATMEGA328P
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC2
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 65 20 4 0 no 1024 4 0 3600 3600 0xff 0xff
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

flash 65 6 128 0 yes 32768 128 256 4500 4500 0xff 0xff
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

lfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

hfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

efuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

lock 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00

Programmer Type : STK500
Description : Atmel STK500 Version 1.x firmware
avrdude: Send: A [41] . [80] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [02]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [81] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [12]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [98] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
Hardware Version: 2
Firmware Version: 1.18
Topcard : Unknown
avrdude: Send: A [41] . [84] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [85] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [86] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [87] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [89] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
Vtarget : 0.0 V
Varef : 0.0 V
Oscillator : Off
SCK period : 0.1 us

avrdude: Send: A [41] . [81] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [12]
avrdude: Recv: . [10]
avrdude: Send: B [42] . [86] . [00] . [00] . [01] . [01] . [01] . [01] . [03] . [ff] . [ff] . [ff] . [ff] . [00] . [80] . [04] . [00] . [00] . [00] . [80] . [00] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: E [45] . [05] . [04] . [d7] . [c2] . [00] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: P [50] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: AVR device initialized and ready to accept instructions

Reading | avrdude: Send: V [56] 0 [30] . [00] . [00] . [00] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: V [56] 0 [30] . [00] . [01] . [00] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
################avrdude: Send: V [56] 0 [30] . [00] . [02] . [00] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
################################## | 100% 0.06s

avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.

avrdude: Send: Q [51] [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]

avrdude done. Thank you.

EDIT 4:
So, I got the same device signature even when I want to burn the bootloader. The -F doesn't change anything, the upload succeed but the programmed arduino is not working.

EDIT 5 :
If I'm programming the atmega328 directly with ICSP (without passing through the arduino board, on a breadboard) the chips are all working. So I think it's coming from the board it self. But as I don't have oscilloscope "only" multimeters and logic analyzer, the troobleshooting will not be easy. If you have any ideas.

#2

Maximum message size reached so...

EDIT 6
If I put the working chip back to the arduino board, I get a voltage on the correct output. But really low and not blinking. But only the output mentionned in the sketch is high. Dead regulator ?

EDIT 7
With the chip on the board. The voltage regulator is ok. The atmega328 AREF is 4.99V, AVCC 4.25V, VCC 4.26V.
Led L attached to D13 is 1.83V.
Measure between D9 on the chip and the ground on the same chip give me 4.8V. Measure between D9 on the chip and D9 pin gives me 2.3V.

EDIT 8
I start to think the problem comes from the ATMega16U2 chip. But the measurements seems ok.
Also I've checked the crystal and he's working too.

EDIT 9
Voltage on the reset pin of the atmega328 always remain high, even when I press the reset button on the uno... (but is correctly goeing to 0 on the button, so button itself is ok)

EDIT 10
After further investigation, the reset pin on the 16U2 isn't set to low when pressing the reset button too. According to the uno schematics I suspect C5 of being dead. RN2D is ok.

EDIT 11
I have re-flashed the ATMega16U2 firmware. Problem persist.

#3

Ok so, after 9h of research I figured out the problem. Since 9h I was putting the chip... (prepare to laugh) in the wrong direction...

I... I'm sorry... really...

And yes you can laugh...

So the answer to that issue is : Put the chip in the correct direction.

#4