This fluctuation seems to be too frequent to be caused by your converter's Charge Wizard, unless it is malfunctioning. Check the voltage at the battery, (it should be around 13.6 volts when the Charge Wizard is operating in Normal Mode) and see what happens to the voltage when your lights dim/brighten. I can't think of another load that could be fluctuating at this frequency. What other 12 volt loads are you running? An inverter (to get 120vac from 12vdc) perhaps? Is your water pump cycling on and off?
You could try shutting off the converter (open the circuit breaker for it in the power centre) and see how the lights fair when supplied from the battery alone. If the lights are more stable then the problem is being caused by the converter. This will also tell you how good your battery really is.