[Mark McLeod]

The description still sounds like a short that only happens when Enabled.

The Relays and PWM signal lines are the only things that are enabled when you enable the robot, and disabled when the robot is Disabled.
The DIOs & RSL keep doing what they are doing in either state, so no change there.
The DSL itself remains a possibility, since some internal circuits could be shorting too. Have you turned it upside down over a clean cheet of paper and given it a shaking to see if metal dust falls out?

I'd still look at pulling all the PWM and Relay connections.
P.S.
A flickering battery light in Disabled is going to mean a bad power connection.
Use a meter on the 12v power input to the DSL to insure you've got battery voltage at that point when Enabled.