Water leaking into rod boxes

This is a topic that has beaten to death, but there may be a reason other than water leaking around the lid some how that can cause this problem.  On our 1997 Pantera Classic the issue was caused by the drain tube from the recessed tray area being stopped up.  This happen due to changing out trolling motors and not being able to pull the old rubber mount back out. I instead knocked them down into the boat with the thought they would come out. What I did not realize is the drain tube is only an out 1".  The pieces ended up getting in the tube and blocking it up.  Because there is an opening to let air circulate in the boat water would fill up the "storage" area under the tray and spill over into the rod boxes. Because my driveway leans to the driver side of the boat the way we park the boat I kept thinking it was an issue with the one locker because the other would not get water in it. Now how I figured out what the problem was and how I fixed it. My son was in a boat wreck that damaged the front of the boat. I decided to remove and look under one of the panels to see the damage from the back side. That was when I discovered the water holding in the area under the tray.  I tried several thing to unblock the drain including a shop vac.  I finally used an heavy solid wire (metal coat hanger) with a little bit of bend on the end and ran it in and out of the tube until I could not feel it hitting anything.  I then flooded the tray with a water hose to make sure it drained like it should.  I had pulled the floor drain so I could see where the tube came out. When I looked there that is when I found the rubber with a nut from the trolling motor mounts. I can see other things being able to fall through the tray drains and getting hung up to block the drain tube. So if you have tried everything else you may want to access under the tray and see if there may be something block the tube. Since our boat was made Bass Cat may have increased the size of this tube so this may not be a possible issue on newer boats.