On our C34 MkII we also had some mud chunks get in the way of adequate drainage. I had to clear things out and literally get to the bottom of things. We then did put a grate in the bottom to help keep the rode up and prevent it from slowing drainage. When I accessed the space below (from the forward cabin), I found that our hose had a slight dip in it before exiting out through the thru-hull. I couldn't shorten the tubing to get the dip out since the real issue was that the outlet was put in just a bit too high relative to the underside of the locker. So we just made sure to adequately flush the locker after every anchor raising, and check on the starboard side to ensure that we saw the water coming out.
Another thing to watch out for, if your boat had been out of the water for a while is to check all your thru-hull fitting before going into the water for wasp/bee nests or other insect homes.