I'm not a fan of their LED based bias system. The bias is supposed to be set at idle so don't be concerned what the LED's are doing when you are playing. There is nothing wrong with the system on the older amps where you measured the cathode current through a 1 ohm resistor.
One thing about any biasing, it is going to change if the line voltage changes. Some venues are notorious for having low voltage. Also some of those power conditioners can limit current into the amp.
It sounds like you are doing it properly but Ampeg has a video where they demonstrate how to set the bias on the CL:
Biasing an Ampeg SVT-CL (http://www.youtube.com/watch?v=aIHKY-OkEJs#ws)
I know it's a pain but I would still pull the power amp and inspect the resistors on the power tube board.