The recorded voltages suggest that the batteries are unbalanced, thus not charging equally.
See page 20,
Fitting these units may help. ( need 3 for a 48v battery)
Equalize the state of charge of two series connected 12V batteries using the Battery Balancer. Find a Victron Energy dealer near you.
www.victronenergy.com
It would also help if the batteries were connected in parallel pairs before the series connection.
Its possible one or more batteries have been damaged/lost capacity. An individual capacity test on each would be useful.
My guess is the batteries have lost capacity due to 'capacity walk down' caused by less than ideal charge and deep discharges.
Mike