With a boat, it could be anything.
For that amount of water though, I'd check around the outdrive (bellows, etc.) first. If you don't already, most people recommend that you store the outdrive down, not up, so that you don't over-flex the bellows.
If it were me, I'd make 100% sure the bilge is dry stem to stern, the go to the launch ramp on a slow day, back the trailer in and look to see if you can find obvious water intrusions.
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