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I have a couple of thoughts based on my Outrage 240.

You might want to taste the water to see if it is freshwater or salty. This can help figure if it is rain or leakage from below...

1) I found that both of my cockpit drains were pretty clogged with debris, including a plastic bag from the previous owner. Any blockage will cause more rainwater to accumulate in the boxes. A plumbing snake fixed this.

2) Check to make sure that your fishbox drainplugs are tight. I've seen mine leak. Theses plugs are almost a foot under the waterline, so there is more pressure than the average stern plug.

3) Check your pumps (impellers as well) and hoses to the macerators. I replaced my pumps and there is maybe a gallon of water left when I've done the pump out. I think the replacements were $80 apiece and took an hour each to replace.

My boat is kept on a lift and the rain water accumulates in the boxes if I leave the plugs in. It is worse if the boat is not perfectly positioned / leveled on the lift. I think it is a design issue. I assume there will be rainwater if I leave the plugs in. It only takes maybe 3 minutes to pump them out if full.