Since the seal and drain appear fine, water might be entering through a small crack or gap that’s hard to spot. Start by inspecting the compartment’s lid and lip where the seal meets…use a flashlight to check for tiny cracks or uneven areas in the sealant. Also, examine the compartment’s corners and edges for any signs of wear or gaps. If you find any, apply a marine-grade sealant like 3M 5200 to those areas. Have you tried testing the compartment with a hose to see if you can spot where the water is getting in?