Sounds almost like you were abducted.. They should have given you your money back.
As for customs you quote:
(Gus had told us that we had to leave our bags on the catamaran and then go back for them after clearing customs. One of the TSA agents asked us why we didn't have our bags with us.)
Usually on a charter or private vessel when checking in your only required to bring your identification and the boat papers. If Customs is suspicious then they'll go to your boat a search it.