I've had a look at some of the saves in that folder. The only problem I can see is that in all of them, you have very little food or rum. If the rum runs out, crew morale will certainly go down. If the food runs out, morale will go down and so will the number of crew because they're starving to death! You can check the food and rum levels - press F2, click on "Ships", then on "Crew", then there should be a button for rations.
The latest of the saves shows your ship with good morale, and a companion sloop with low morale, probably because it has no food. There is also an active ship-hunting quest. I sold the sloop, went after the ship in the quest, sank it with cannon fire, then returned to the governor to claim the reward. Winning a sea battle improves morale, so the crew's morale went up to 73. After stocking up on food and rum, I sailed the whole way from Jamaica to Barbados. Morale dropped to 72, which is probably your normal maximum with your current "Leadership" skill; it did not drop any further and was still 72 when I arrived at Barbados.
By the way, you have not equipped your compass or clock. You also still have the cheap, nearly useless spyglass. Go to a street trader and see if you can get something better. (In the latest of your saves, the nearest street trader in Kingston port certainly has a better spyglass, as well as an enhanced compass and a chronometer, and when you've sold the sloop, you can afford to buy them as well as a good load of food and rum. This I know because I bought them all.
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