I would place a block of wood under the tounge jack of the trailer, then block the wheels of the trailer, then crank it as high as I could to elevate the front of the boat. Next I would get a garden hose and put water in the compartment to see if it came out the back of the boat's bilge drain hole. After only a few seconds, you should have water appear if the drain is in fact clear and free flowing.
If you don't get any water, or only a "trickle", locate a "Fish Tape" used in electrical work. You can purchase a cheap one from Harbor Freight or Lowe's for less than $20. Run this steel tape down the drain from the compartment towards the transom. You may have a pile of fish scales that have dried, or a label from a water bottle, or any number of things stopping it up. If this doesn't solve the mystery, I would bring it to a local fiberglass shop and have them take a peak. They will surely find the problem, then you can address it!
Hope that helps and let us know what you find!