I will try to connect 86 to GND and let you know.
Voltage shouldn’t go over 14.4V so I think it is fine
Still strange behaviour of pwm duo that it doesn’t fully charge battery 1 as set
Ok, let’s try to solve the first issue, then we take care for the PWM controller. 
I can see now alternator voltage on both batteries 
1 Like
YES 
Maybe you can check if the relais is connecting (closing the contact) in the given timeframe.
But I guess this will work now correct.
And now we can tackle the second problem with the PWM Charge controller.
Please show/tell us how you did connect the batteries?
I have a suspicion, - you are loading both batteries from the PMW controller, right?
First I connected battery 1 (pos then neg), then battery 2 (pos then neg) and solar panel (pos then neg).
Yes, I am charging both batteries as this is pwm duo controller
I just checked the Datasheet of the PWM Duo Controller.
And your connection order is as described, so the system should automatically detect a 12V system. And I guess your other settings for AGM and floated acid battery is correct.
Now it i up to the capacity of the batteries and the remaining state of charge how long the 80/20 current distribution needs to charge both batteries.
If you give the solar controller enough time, then both batteries are finally full, right?
The only thing is, that you do not use the bi-directional function of the cyrix ct relais.
So please check now, if with the correct connection of the relais the problem is still existing.
When I switch off engine, I switch off battery switch as well so cyrix doesn’t have any input and shuts down immediately
I can see both batteries are fully charger but the voltages are not same, it is charging batt2 more than batt 1 as preference set
Which settings did you set up in the controller?
80/20
Ok, but which battery profiles did you select? You can choose between AGM and other different types of batteries.
This setting will then provide the needed absorbtion voltage for each battery.
Edit:
You should have b01 for the AGM and b03 for the starter battery.
Check the manual for the solar controller.
But how to choose type of battery? B01 is my AGM
Please read the manual, I don’t have this controller, I just saw it in the manual.
If you select the correct type of battery for your setup, I assume it will work.