Do you have blue/red LEDs for multiple banks, and are all blinking or just one set? Often, such blinking means a safety fault such as a battery discharged below 10.5 volts. Most smart chargers won't recognize or charge such a battery. This may mean you have a battery that's basically ready for a recycle.
If you have a voltmeter, and multiple banks, check the charging voltage of each battery. A good battery being charged should read over 13 volts, typically ~13.5V. If you have one bank that's a lot lower, you can unplug, switch the charger leads between batteries as pairs, then plug it in and meter again. If the low voltage still reads on the same battery, the battery is bad. if the low voltage moves to the other battery, the charger output is bad.