Hi Lee,
I was going to suggest there was probably a drain in the bottom of it that most likely just drains the water back to the bilge. Seems like you've already got that figured out. Most ski lockers work the same way as well.
I know it's not uncommon for those types of drains to be somewhat smallish and they can therefore get plugged up pretty easily. Sometimes running a hose with clean water is enough to clear out any debris and get things flowing normally again.
I'm not sure if yours would benefit from that or if it's more of a design issue.
If you like, upload some pictures of your boat in the gallery and then we can link them and post them here.
I gather it's a Sea Ray? Hope so.
If not, let me know who makes it.
I created a Sea Ray category for you in the gallery where you can upload the pics.
-Chris