It may be the charger or it may be the battery. Discharging a SLA battery significantly below 50% of its capacity will most likely cause permanent damage that will manifest itself as reduced capacity and/or an inability to accept a full charge. Try the charger with a known good battery, or try charging the battery with a charger you know is good, then test it's capacity. Here's a chart of (no load) voltage vs. approx. capacity for lead acid batteries:

Lead Acid No Load Voltage vs. Capacity

12.65 = 100%
12.45 = 75%
12.24 = 50%
12.06 = 25%
11.89 = 0%