Battery Charging Properly

The batteries are full, they are at 14.4V according to the SmartShunt and the MPPT is saying it is pretty full. I do not think you have a charging issue, I think you have a SmartShunt measuring issue not measuring the solar input so it is not increasing, nor setting to 100%. I have a feeling that you have connected the negative wire from the MPPT direct to the battery negative, this wire needs to go to the SmartShunt system terminal so the current flows through the SmartShunt so it can be measured. See