is the water going into the inlet without resistance? the only other explanation would be exactly what kaykay said. how much are you exactly topping?
happened to me once. half of my 1ft tank water suddenly disappeared. finally traced to improper priming. shook the canisters for some time and ended up 3/4 of my tank water gone before canisters were fully primed.
if there's no leak, topping up of water doesn't really hurt, of course, salinity must match.