Any idea what alternator you have? Are you running a voltmeter or an ammeter?
Here is a little test to try and narrow it down. Run a 10 gauge wire from the post on the alternator to the positive side of the battery and run it again.
If it wired in the conventional sense, the power from the alternator goes to an orange wire, all the way to the dash and back. these wires would traditionally go "through' an ammeter and they would typically have a 35 am alternator.
On most boats, they use an internally regulated alternator, the exciter wire is the voltage typically to the dash ign. wire. This tells the alternator the condition of the charge. If the alternator is seeing too low of voltage from the exciter wire, the alternator will full field and definitely cause the breaker to trip. It may not do it when the boat is "cold" because the battery has not yet reached full charge.
I am grasping at straws here, but this experiment wont hurt anything and is totally reversible.
GT