Been messing around with this at lunchtime today, removed all inductors and capacitors from the amplifier card to eliminate anything there.
I fired the amp up and still a fair bit of current being drawn, reset line on processor card still being pulled low by the watchdog IC every 1.2 seconds.
Decided to have a poke around the board with the scope, noticed the processors were doing "something" so tried the thermal camera on the processor card.
Noticed the EEPROM cooking itself! Checked the 5V rail and found it to be over 9V!
Anyway long story short... The component getting hot on the amplifier card in the corner was the MOSFET for the 5V power supply. When I originally started testing the card the output voltage from the MOSFET circuit was 12V, I didn't think this was abnormal. Little did I know it should have been 5V!
Luckily the three processors and RAM all run on 3.3V and have not been over voltaged.
I therefore tried running the processor card from a separate 5V bench supply.
This provided some hopeful results, the processor is now kicking the watchdog IC and it's no longer resetting every second or so.
I will investigate whats going on with the 5V supply and take it from there.
There is a slim chance it's repairable if the EEPROMS are not damaged. (I don't have the code, and I can't imagine it's easy to get hold of!)