If you never noticed 16 volts before when you previously looked then you may have a regulator as they usually limit the peak voltage to 14.5 v, above 1000 rpm. A non-regulated supply runs 16 volts above 1000 rpm (says the op. manual). If the two big batteries you installed were in a serious state of discharge you may have burned out the regulator. Charging circuits are made to "maintain" a previously charged battery, not charge them from scratch. Smoking gun for the regulator would be heat destroying the regulator components.
Mark