A very rare occurrence could be that your PH is swinging drastically when the lights go out. When the lights are on photosynthetic algaes are using up the available CO2 and producing O2 as waste. O2 is a good thing to have in your tank. At night, without the lighting, the algae becomes dormant allowing CO2 to build in concentrations that can react with other minerals in the tank. This in turn can cause drastic PH drop outs. You will read about a lot of folks keeping a light on the sump under the tank running for 24 hours. This keeps light and alga in another part of the tank.
You don't give enough information about the set up to really give appropriate answers. Could you tell us more about the system? Examples being, is it a reef tank, fish only, what equipment do you have running?