The first thing you should check is the regulator output setting to see if measured voltage is consistent and do so when the batteries are NOT fully charged.
Additionally, make sure the Link20 rate is properly set and calibrated.
Regardless of the varying opinions with respect to battery configuration between Steve and me, no one can contest the over-riding benefit to combine the two larger batteries as a large house bank. Having a separate 200 amp start battery is overkill when compared with your present 300 amp "Position 1" house bank .
The larger the house bank, the smaller the discharge rate resulting in prolonging the life of the batteries.