#1. Never trust that your charger is working properly. Always verify that it is actually working to specification.
#2. Take the time to properly test and charge each battery in a bank BY ITSELF without any other batteries connected. Test specific gravity and open circuit voltage after the battery has been disconnected for 12 hours or more. Connect the battery to the charger, and monitor the charging voltage every hour. After the charging cycle is complete, disconnect the battery and let it sit for 12 hours or more. Recheck Specific gravity and open circuit voltage.
ONLY THEN can you evaluate the TRUE CONDITION of each battery. Yes it is a bit of work, but then you won't just be "Shooting in the dark"
Link to details:
Battery Maintenance | Trojan Battery Company