As the author of the guide, the most common problem is the sync to 100% occurring too early. It could also occur too late but the recommendations apply regardless.
There are other settings that are different for AGM and lithium, Peukert for lithium should be 1.05 and charge efficiency 0.99, these both affect the SOC calculation.
Another reason for under reading is a zero error so it is measuring a phantom load, do a zero current calibration, the procedure is in the manual.
Finally, the wiring may be at fault, see this additional FAQ, but if so you would have had issues with lead acid also.