Just re-posting this here, since this topic is on two different thread/boards.
I have a similar problem. I removed the original two l stainless steel tanks this past winter and replaced them with a single smaller plastic tank. When I had the tanks out I could see a small hole at the back of the center bilge which leads to the compartment where I have the aft bilge pump. Unfortunately when I filled the new tank the inlet pipe leaked and I ended up with about 40 litres of water in the center bilge compartment. I couldn't get the center bilge compartment to drain despite pushing a rod through the hole, from the aft bilge, as far as I could. Possibly it's blocked but no matter what I tried I couldn't get it to drain. I ended up using a sponge to mop up as much water as I could and was going to leave it till the next haul out to deal with it properly. So I've got a few inches on my center bilge right now.
If you put your hand in the aft bilge you should be able to feel the hole at the very bottom of the bilge. I was wondering if the issue is that my rear bilge pump float was so high, and the bilge so large, that the water level never gets high enough to trigger the bilge pump. That's the only idea I have right now. Maybe some others can provide some more information about this.