I don't know how many times I've cleared into the BVI in the past - certainly over 50 times. I don't think that I've ever paid the same amount twice.

I think that your entry visa is limited to 28 days, while the boat can remain longer. I've found that purchasing a "temporary import" (required if the boat stays in the BVI longer, e.g. for storage during the hurricane season) for around US$150 per year has made a difference to my clearing-in and clearing-out fees.

But you have another potential problem that can be quite expensive. Your boat is a charter boat in the USVI. When you come to the BVI they can treat the boat as a foreign charter vessel and charge charter fees. Even if you are the owners. I was clearing in to Spanish Town once and 4 French people ahead of me were in that situation. One couple were owners and the other were friends. The boat was in a charter fleet in St. Martin. The officials charged them over US$1000, I believe it 1500, for one week. They argued for quite a while but in the end had to pay the fees as the alternative would have been to sail back upwind to SXM (non-Americans need a visa to sail to the USVI and all of them didn't have one). This despite having clear paperwork.