"Little update on my case : I've reflashed the 328P with an AVRDragon programmer, went fine. I've reset the EEPROM of the ardupilot, and after many tests, here is the status : 

All radio input channels are to zero exempt channel 1 which works fine…"

"small update : i'm waiting for the programmer to arrive to reprogram the chip...
 
Marianne> what happened to the boards since ? have they magically worked again ? "

"i've been using it on some previous quadcopters, it works fine, but breaks on crash, however every time i had a serious crash some part of the structure broke, whatever material :)"

"I may be interested. in which part of the uk are you ? (i am in east anglia).
 
thanks, "

"nobody has a clue for me ? :/ thanks,
 "

"fixed, see http://diydrones.com/forum/topics/gps-issues-with-shared-power-help...:)"

"False alert : problem is not sorted out !!!! :)
 
Here's a quick update on the tests and the findings : 

USB connected, APM powered via RC rail by 4AA batteries, no ESC attached : GPS blinking blue, LED B steady and C blinking (red)
USB…"

"The receiver is a graupner R16Scan, and it's quite far from the APM. Will try without it, but manual flying might be a bit difficult ;) I will also try a diffrent powersupply for RC rail and the APM, just in case. 
 "