First of all do both glow plug come on and glow brightly? If so then it is likely a problem in the new glowplug sensing software. If not then the slow flashing red LED thinks there is not a glow plug or battery connected.

You have version 2.1. Glowdriver LEDs operate different on 2.1 than 2.0. On 2.1 (that you have) If you do not have a plug and/or battery connected the red leds on the sync will flash slowly. If the glow battery is low they will flash fast. If everything is good then they will be on solid. I have not released this new version of software to production units yet. I am still tweaking some of the voltage thresholds. The led on the glowdrivers will always be on solid when glow drivers are on.

So if every thing is working correctly except for the red slow flshing led, can you email me the voltage you read on the orange wire of that glowdriver when plugs are turned off and plugs are on?