Sounds like a "system" issue.
Connector CN1 is where most of your LEDs are controlled by a CPLD IC which is obviously latched.
Just about all you can do is to check for all your regulated voltages(3,5,9..etc) on CPU main board. Any of the failed regulators could cause this.
Also there are several oscillators & don't forget the RESET signal and any data line activity(preferably with a scope).
And if they are all there, it is likely you may be facing unobtainable corrupted software?