If it is a new boat, and water stays in the bowl over night (your comment that you have to put a lot of water in the bowl is confusing in this regard), then it may be that someone has already flushed something they shouldn't have. It's not backing up is it? Try filling the bowl and holding the lever down for a long time, say 15 seconds. Oftentimes this will clear the valves for you. As mentioned above, whenever flushing do let the foot pedal up with your foot on it, pull your foot away when it is fully depressed (and remember hold down to the count of three for liquid waste, 10 for solids!) and let it snap up hard.
If the bowl is draining water between flushes, after cleaning around the seal as per the instructions (actually I just use my finger and not the little wood stick), wipe some silicon grease around the bottom the seal where it interfaces with the ball valve . Courtesy of GeeBee (Greg) this may be the single best piece of advice I have received on this forum. We do this maybe a couple times a year (full time liveaboards) and these toilets give us less hassle than the ones we had on land.
George
Hatteras 56MY (three independent VFs on board).