I would check the plug connections on the power distribution board and power supply.. I had a V2000 doing some strange things.. I never really found the problem, but I did unplug all the both boards and plug them back together and my problem stopped.. Those pin connectors do tarnish.. Hopefully yours is that simple.. The other thing to check would be your edge connector plugs on the 3 board stack, those connection go bad from heat cycles.. Other possible is that your have developed a bad solder connection on one of your boards sockets, or other IC's..
Gary