I’ve had a chance to look into this further, and have some suggestions for how to configure the mains. Although I remain skeptical that your meter reads VA rather than Watts, this should make both units measure correctly.
Being unfamiliar with this type of service, I fell back on how commercial meters approach this. I found this to very helpful.
First, you should be sure that all three of the CTs on the mains are oriented the same way. You have designated your Mains to be Main_A, Main_B and Mains_C. Please verify that the AC reference transformer is connected to Main_A to neutral.
It’s not possible for me to know the phase rotation of you B and C mains, but there are only two possibilities and if this doesn’t work quite right, we’ll just try the other.
This is where it’s going to get tricky. Assuming that Mains_A to Mains_C is the split phase and Mains_B is the “high-leg” (208V - neutral), please assign the following phase references:
Mains_A -> Phase A
Mains_B -> Phase B-C
Mains_C -> Phase A and check the “reverse box”
These changes will not correct your history to date. They should cause the correct measurements to be made going forward. So first indications would be to look at the status and see if the real-time Watts are reasonable (post if possible). Also, start a log recording your meter kWh and the date/time of the reading. We will use this as the ultimate validation tool.