Customs is not open for commercial boats in West End. All ferries must go to Roadtown. Looks like with the politics involved it may be a long term situation.
Is that schedule reliable? When I enter into the companies website, the schedule is different. I will arrive to STT at 12.30 PM, which ferry should I take to RT and JVD?
Really the answer is take the first one that is leaving. Once you get to Road Town you will have to take a taxi to the West End and catch the JVD ferry. So you will likely take the 2:30 out of Charlotte Amalie to Roadtown, and then the 6:00 out of West End to JVD.