Doesn't sound like anything is wrong here. Batteries are being charged by the highest current source, which is your generator by way of the Magnum. If it was raining, there's not much solar radiation, your panels won't be doing anything but a trickle charge anyway.
Obviously, the magnum detected the battery temperature was low and adjusted the charging voltage to compensate for that. The BlueSky doesn't have temperature compensation? Seems like a must-have feature for any large or outdoor battery bank.
On your ARC remote, what does the CHARGER button do for the hybrid inverter? Can you turn off the charger on the hybrid, while it is powering loads is what I'm wondering?